[R] degrees of freedom
Hello List I have been asked to analyse some data for a colleague. The design consists of a two sets of animals First set of three - one leg is treated and the other is not under two different conditions (control overload are the same animals - control leg is control (!) for treated leg; Second set of three - one leg is treated and the other is not under two different conditions (high_fat and high_fat_overload are the same animals with high_fat being control leg for high_fat_overload). Ideally I'd like to find differences between the treatments. bip - structure(list(group = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L), .Label = c(control, overload, high_fat, high_fat_overload), class = factor), variable = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label = BiP, class = factor), animal = structure(c(1L, 3L, 5L, 1L, 3L, 5L, 2L, 4L, 6L, 2L, 4L, 6L), .Label = c(rat1_c, rat1_hf, rat2_c, rat2_hf, rat3_c, rat3_hf), class = factor), value = c(404979.65625, 783511.8125, 677277.625, 1576900.375, 1460101.875, 1591022, 581313.75, 992724.1875, 1106941.5, 996600.375, 1101696.5, 1171004.375)), .Names = c(group, variable, animal, value), row.names = c(NA, 12L), class = data.frame) I chose to analyse this as a mixed effects model with treatment as a fixed effect and animal as random. library(lme4) model1 - lmer(value~group + (1|animal), data=bip) summary(model1) And then compare this to no treatment with: anova(model1) From this I wanted to work out whether 'treatment' was significantly affecting BiP levels by calculating the critical value of F for this design. I have 2 groups of animals and 3 animals per group. My calculation for the degrees of freedom for treatment is 4-1=3. I'm not sure about the degrees of freedom for the denominator though. Since I'm comparing a model with treatment to one without (i.e. the grand mean) would the df for my denominator be 6-1=5? So I'd then have: qf(0.95,3,5) for my critical F value? Best iain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] heatmap tile size question
Hello List I was wondering if it is possible to make the individual 'tiles' in a heatmap larger. Often when I plot heatmaps and want to label the rows with eg gene names I either have to shrink the text or leave it out altogether as it becomes so small as to be unreadable. I wondered if there was a way to make the 'tiles' deeper and therefore allow more room for the row labels. I apologise if this is not entirely clear but the toy code below might illustrate the problem. library(hgu133plus2.db) # fake up some data testMat - matrix(rnorm(4500, 4, 2), 150, 30) testMat[,15:30] - testMat[,15:30]*4 # clear differnce geneNames - as.list(hgu133plus2SYMBOL) # get some gene names rownames(testMat) - stack(sample(geneNames, 150))[,1] # relabel the matrix heatmap(testMat) # row labels overlap Best Iain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] write out list of lists with names
Hello List
I have a list question. I'm doing some data wrangling for a colleague and I
have nested list in the following format:
structure(list(MU10 = structure(c(0.80527905920989, 0.4350488707836,
0.455195366623, 0.565174432205497, 0.208180556861924), .Names = c(MU.16,
MU.19, MU.21, mean, sd)), MU11 = structure(c(0.56061565798878,
0.65200918021661, 0.606312419102695, 0.0646249793238221), .Names = c(MU.21,
MU.22, mean, sd)), MU12 = structure(c(0.77265115449472,
0.3925776107826, 0.38222435807226, 0.515817707783193, 0.222484520748552
), .Names = c(MU.14, MU.20, MU.23, mean, sd)), MU13 =
structure(c(0.36360576458114,
0.21396125968483, 0.288783512132985, 0.105814644179484), .Names = c(MU.20,
MU.22, mean, sd)), MU14 = structure(c(0.31692017862428,
0.31692017862428, NA), .Names = c(MU.18, mean, sd)), MU15 =
structure(c(0.57645424339545,
0.82369227173036, 0.700073257562905, 0.174823686402807), .Names = c(MU.18,
MU.22, mean, sd))), .Names = c(MU10, MU11, MU12,
MU13, MU14, MU15))
I would like to write this to a text file in the form e.g. (each x is a value):
MU10
MU.16 MU.19 MU.21 mean sd
x x x x x
MU11
MU.21 MU.22 mean sd
x x x x
Where each list element is on a new block of three rows.
After consulting Google I came across the following:
fnlist - function(x, fil){
z - deparse(substitute(x))
cat(z, \n, file = fil)
nams - names(x)
for (i in seq_along(x) ){ cat(nams[i], \n, x[[i]], \n,file = fil, append =
TRUE) }
}
fnlist(holdList, 'res.txt')
However this doesn't print the names within each sub list.
Can anyone advise?
Thanks
Iain
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plyr_1.7.1 gsubfn_0.6-5 proto_0.3-9.2
loaded via a namespace (and not attached):
[1] tcltk_2.15.1 tools_2.15.1
Iain
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] conditional subset and reorder dataframe rows
Hi List
I have a dataframe (~1,200,000 rows deep) and I'd like to conditionally reorder
groups of rows in this dataframe.
I would like to reorder any rows where the Chr.Strand column contains a '-' but
reorder within subsets delineated by the Probe.Set.Name column.
# toy example
library(plyr)
negStrandGene - data.frame(Probe.Set.Name = rep('ENSMUSG0022174_at', 6),
Chr = rep(14,6), Chr.Strand = rep('-', 6), Chr.From = c(54873546, 54873539,
54873533, 54873529, 54873527, 54873416), Probe.X =
c(388,1634,2141,2305,882,960), Probe.Y = c(2112, 1773, 1045, 862, 971, 2160))
posStrandGene - data.frame(Probe.Set.Name = rep('ENSMUSG0047459_at', 6),
Chr = rep(2, 6), Chr.Strand = rep('+', 6), Chr.From = c(155062277, 155062304,
155062305, 155062309, 155062326, 155062531), Probe.X = c(428, 1681, 2058, 1570,
1293, 2125), Probe.Y = c(1484, 2090, 893, 1082, 1435, 1008))
mapping - rbind (negStrandGene, posStrandGene)
# define a function to do what we want
revSort - function(df){
if (unique(df$Chr.Strand == '-'))
return (df[order(df$Chr.From), ])
else return (df)
}
# split the data with plyr, apply the function and recombine
test2 - ddply(mapping, .(Probe.Set.Name), function(df) revSort(df)) # ok, cool
works
So here the rows with the '-' if Chr.Strand are reordered whilst those with '+'
are not.
My initial attempt using plyr is very inefficient and I wondered if someone
could suggest something better.
Best
Iain
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] reading file in zip archive
Hi Phil
That's it. Thanks.
Will have a read at the docs now and see if I can figure out why leaving the
'r'ead instruction out works. Seems counter-intuitive!
Best
Iain
From: Phil Spector spec...@stat.berkeley.edu
To: Iain Gallagher iaingallag...@btopenworld.com
Cc: r-help r-help@r-project.org
Sent: Thursday, 31 May 2012, 0:06
Subject: Re: [R] reading file in zip archive
Iain -
Do you see the same behaviour if you use
z - unz(pathToZip, 'x.txt')
instead of
z - unz(pathToZip, 'x.txt','r')
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Wed, 30 May 2012, Iain Gallagher wrote:
Hi Phil
Thanks, but this still doesn't work.
Here's a reproducible example (was wrapping my head around these functions
before).
x - as.data.frame(cbind(rep('a',5), rep('b',5)))
y - as.data.frame(cbind(rep('c',5), rep('d',5)))
write.table(x, 'x.txt', sep='\t', quote=FALSE)
write.table(y, 'y.txt', sep='\t', quote=FALSE)
zip('test.zip', files = c('x.txt', 'y.txt'))
pathToZip - paste(getwd(), '/test.zip', sep='')
z - unz(pathToZip, 'x.txt', 'r')
zT - read.table(z, header=FALSE, sep='\t')
Error in read.table(z, header = FALSE, sep = \t) :
seek not enabled for this connection
As I said in my previous email readLines fails as well. Rather strange really.
Anyway, as before any advice would be appreciated.
Best
Iain
_
From: Phil Spector spec...@stat.berkeley.edu
To: Iain Gallagher iaingallag...@btopenworld.com
Cc: r-help r-help@r-project.org
Sent: Wednesday, 30 May 2012, 20:16
Subject: Re: [R] reading file in zip archive
Iain -
Once you specify the file to unzip in the call to unz, there's no
need to repeat the filename in read.table. Try:
z - unz(pathToZip, 'goCats.txt', 'r')
zT - read.table(z, header=TRUE, sep='\t')
(Although I can't reproduce the exact error which you saw.)
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Wed, 30 May 2012, Iain Gallagher wrote:
Hi List
I have a series of zip archives each containing several files. One of these
files is called
goCats.txt and I would like to read it into R from the archive. It's a simple
tab delimited text
file.
pathToZip
-'/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2
hrs.zip'
z - unz(pathToZip, 'goCats.txt', 'r')
zT - read.table(z, 'goCats.txt', header=T, sep='\t')
Error in read.table(z, goCats.txt, header = T, sep = \t) :
? seek not enabled for this connection
The same error arises with readLines.
Can anyone advise?
Best
iain
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
?[1] LC_CTYPE=en_GB.utf8?? LC_NUMERIC=C
?[3] LC_TIME=en_GB.utf8??? LC_COLLATE=en_GB.utf8???
?[5] LC_MONETARY=en_GB.utf8??? LC_MESSAGES=en_GB.utf8??
?[7] LC_PAPER=C??? LC_NAME=C???
?[9] LC_ADDRESS=C? LC_TELEPHONE=C??
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C?
attached base packages:
[1] stats graphics? grDevices utils datasets? methods?? base
loaded via a namespace (and not attached):
[1] tools_2.15.0
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] reading file in zip archive
Hi List I have a series of zip archives each containing several files. One of these files is called goCats.txt and I would like to read it into R from the archive. It's a simple tab delimited text file. pathToZip - '/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2hrs.zip' z - unz(pathToZip, 'goCats.txt', 'r') zT - read.table(z, 'goCats.txt', header=T, sep='\t') Error in read.table(z, goCats.txt, header = T, sep = \t) : seek not enabled for this connection The same error arises with readLines. Can anyone advise? Best iain sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.15.0 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reading file in zip archive
Hi Phil
Thanks, but this still doesn't work.
Here's a reproducible example (was wrapping my head around these functions
before).
x - as.data.frame(cbind(rep('a',5), rep('b',5)))
y - as.data.frame(cbind(rep('c',5), rep('d',5)))
write.table(x, 'x.txt', sep='\t', quote=FALSE)
write.table(y, 'y.txt', sep='\t', quote=FALSE)
zip('test.zip', files = c('x.txt', 'y.txt'))
pathToZip - paste(getwd(), '/test.zip', sep='')
z - unz(pathToZip, 'x.txt', 'r')
zT - read.table(z, header=FALSE, sep='\t')
Error in read.table(z, header = FALSE, sep = \t) :
seek not enabled for this connection
As I said in my previous email readLines fails as well. Rather strange really.
Anyway, as before any advice would be appreciated.
Best
Iain
From: Phil Spector spec...@stat.berkeley.edu
To: Iain Gallagher iaingallag...@btopenworld.com
Cc: r-help r-help@r-project.org
Sent: Wednesday, 30 May 2012, 20:16
Subject: Re: [R] reading file in zip archive
Iain -
Once you specify the file to unzip in the call to unz, there's no
need to repeat the filename in read.table. Try:
z - unz(pathToZip, 'goCats.txt', 'r')
zT - read.table(z, header=TRUE, sep='\t')
(Although I can't reproduce the exact error which you saw.)
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Wed, 30 May 2012, Iain Gallagher wrote:
Hi List
I have a series of zip archives each containing several files. One of these
files is called goCats.txt and I would like to read it into R from the
archive. It's a simple tab delimited text file.
pathToZip -
'/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2hrs.zip'
z - unz(pathToZip, 'goCats.txt', 'r')
zT - read.table(z, 'goCats.txt', header=T, sep='\t')
Error in read.table(z, goCats.txt, header = T, sep = \t) :
? seek not enabled for this connection
The same error arises with readLines.
Can anyone advise?
Best
iain
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
?[1] LC_CTYPE=en_GB.utf8?? LC_NUMERIC=C
?[3] LC_TIME=en_GB.utf8??? LC_COLLATE=en_GB.utf8???
?[5] LC_MONETARY=en_GB.utf8??? LC_MESSAGES=en_GB.utf8??
?[7] LC_PAPER=C??? LC_NAME=C???
?[9] LC_ADDRESS=C? LC_TELEPHONE=C??
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C?
attached base packages:
[1] stats graphics? grDevices utils datasets? methods?? base
loaded via a namespace (and not attached):
[1] tools_2.15.0
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Completely Off Topic:Link to IOM report on use of -omics tests in clinical trials
I followed this case while it was ongoing. It was a very interesting example of basic mistakes but also (for me) of journal politicking. Keith Baggerly and Kevin Coombes wrote a great paper - DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY in The Annals of Applied Statistics (2009, Vol. 3, No. 4, 1309–1334) which explains some of the background and investigative work they had to do to bring those mistakes to light. Best iain - Original Message - From: Bert Gunter gunter.ber...@gene.com To: r-help@r-project.org Cc: Sent: Monday, 26 March 2012, 19:12 Subject: [R] Completely Off Topic:Link to IOM report on use of -omics tests in clinical trials Warning: This has little directly to do with R, although R and related tools (e.g. sweave and other reproducible research tools) have a natural role to play. The IOM report: http://www.iom.edu/Reports/2012/Evolution-of-Translational-Omics.aspx that arose out of the Duke Univ. genomics testing scandal has been released. My thanks to Keith Baggerly for forwarding this. I believe that many R users in the medical research community will find this interesting, and I hope I do not venture too far out of line by passing on the link to readers of this list. It **will** have an important impact on so-called Personalized Health Care (which I guess affects all of us), and open source analytical (statistical) methodology is a central issue. For those interested, try the summary first. Best to all, Bert -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hgu133plus2hsentrezgprobe library
Hi Eleni Question like this are better served on the bioconductor mailing list. Nonetheless try this ALL - topTable(fit2, coef=1, number=Inf) ALL$SYMBOL - unlist(mget(ALL$ID, hgu133plus2hsentrezgSYMBOL, ifnotfound=NA)) Here ALL is the output from limma for differential expression (ALL$ID is the probe on ENTREZ centric cdf from brainarray). Best Iain - Original Message - From: Eleni Christodoulou elenic...@gmail.com To: r-help@r-project.org Cc: Sent: Monday, 19 March 2012, 18:47 Subject: [R] hgu133plus2hsentrezgprobe library Hello R community, I am processing raw Affymetrix CEL files and I am using the Michigan custom CDF library hgu133plus2hsentrezgprobe. I have been looking for documentation on the function that it contains...I am specifically interested in converting probe names to gene symbols. Does anybody know where I can find it? Thank a lot! Eleni [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2 reorder factors for faceting
Dear List
I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my
data by 'infection' of which I have four. These four infections break down into
two types and I would like to reorder the 'infection' column of my data to
reflect this.
Toy example below:
library(ggplot2)
# test data for ggplot reordering
genes - (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4),
rep('f',4)) ,4))
fcData - rnorm(96)
times - rep(rep(c(2,6,24,48),6),4)
infection - c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD',
24))
infType - c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))
# data is long format for ggplot2
plotData - as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times),
infection, infType))
hp2 - ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill =
scale(as.numeric(fcData + facet_wrap(~infection, ncol=4)
# set scale
hp2 - hp2 + scale_fill_gradient2(name=NULL, low=#0571B0, mid=#F7F7F7,
high=#CA0020, midpoint=0, breaks=NULL, labels=NULL, limits=NULL,
trans=identity)
# set up text (size, colour etc etc)
hp2 - hp2 + labs(x = Time, y = ) + scale_y_discrete(expand = c(0, 0)) +
opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle =
360, hjust = 0, colour = grey25), axis.text.y = theme_text(size=10, colour =
'gray25'))
hp2 - hp2 + theme_bw()
In the resulting plot I would like infections infA and infC plotted next to
each other and likewise for infB and infD. I have a column in the data -
infType - which I could use to reorder the infection column but so far I have
no luck getting this to work.
Could someone give me a pointer to the best way to reorder the infection factor
and accompanying data into the order I would like?
Best
iain
sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6
loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-Studio Question
Above the graph on the left there are back and forward arrows. You can use those (like a browser). This might have been better asked on the R-Studio forums. They're very friendly. best iain --- On Tue, 30/8/11, Eran Eidinger e...@taykey.com wrote: From: Eran Eidinger e...@taykey.com Subject: [R] R-Studio Question To: r-help@r-project.org Date: Tuesday, 30 August, 2011, 8:59 Hello, I've switched to R studio from the StatET Eclipse plug-in. I have a question regarding navigating between plots. When I use x11() or windows() new devices are created and I know how to switch back and forth between them. However, when I plot on the device that stands for R-Studio's built-in plot browser, is there a way to switch back between plots? Each new plot command opens a new plot, and the number of devices does not change. Thanks, Eran. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Synchronizing R libraries on N machines?
Hi Giovanni Using Ubuntu and MacOSX may not be irrelevant. I use Ubuntu and if I carry out a fresh install (e.g. after a new release - although I've stuck with 10.04 so far) then I always have to mess around, check the web etc to install external packages that R libraries I want to use rely on. A good example would be libxml2-dev (which doesn't appear if you use Synaptic and search for xml2 - sigh) for using biomaRt etc etc. Just a heads up that the external software some R libraries rely on might not be installed on both systems. So installing a package on one system sucessfully doesn't mean you can alway expect it to install without incident on another. Best iain --- On Fri, 26/8/11, Giovanni Petris gpet...@uark.edu wrote: From: Giovanni Petris gpet...@uark.edu Subject: Re: [R] Synchronizing R libraries on N machines? To: Rainer M Krug r.m.k...@gmail.com Cc: r-help@r-project.org Date: Friday, 26 August, 2011, 14:05 Hi Rainer, This certainly helps, but it still requires to do some work by hand. I was hoping for something more automatic - but so far nobody has suggested a better approach. Thank you, Giovanni On Thu, 2011-08-25 at 15:43 +0200, Rainer M Krug wrote: On Thu, Aug 25, 2011 at 3:25 PM, Giovanni Petris gpet...@uark.edu wrote: Hello! I am using R on two different machines (under Ubuntu and OS X, but this is probably irrelevant) and I would like to keep the two installations 'synchronized', in particular in terms of installed packages. For example, if I install package xxx on my Linux machine, I would like to find it installed also on my Mac, and vice versa. I imagine this to be a fairly common problem, so I would like to ask if anybody has suggestions to share about it. Is there a way to make the synchronization automatic? Painless? library()$result[,1] returns the names of the installed packages. If you do this on one machine, then compare it with the same outpout on the other machine, you can identify the packages which are not installed, and you can install those. e.g.: x - letters[1:10] y - letters[5:20] lx[!(x %in% y)] returns a b c d which are in x, but not y. Hope this helps, Rainer returns the letters which are in Thank you in advance for the suggestions. Best, Giovanni -- Giovanni Petris gpet...@uark.edu Associate Professor Department of Mathematical Sciences University of Arkansas - Fayetteville, AR 72701 Ph: (479) 575-6324, 575-8630 (fax) http://definetti.uark.edu/~gpetris/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax (F): +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] aggregating data
Hi Max
Using plyr instead of rehsape:
library(plyr)
df - data.frame(gene=c('A', 'A', 'E', 'A', 'F', 'F'), probe = c(1,2,3,4,5,6))
ddply(df, .(gene), function(df)length(df$gene))
gene V1
1A 3
2E 1
3F 2
best
iain
--- On Thu, 30/6/11, Max Mariasegaram max.mariasega...@qut.edu.au wrote:
From: Max Mariasegaram max.mariasega...@qut.edu.au
Subject: [R] aggregating data
To: r-help@r-project.org r-help@r-project.org
Date: Thursday, 30 June, 2011, 8:28
Hi,
I am interested in using the cast function in R to perform
some aggregation. I did once manage to get it working, but
have now forgotten how I did this. So here is my dilemma. I
have several thousands of probes (about 180,000)
corresponding to each gene; what I'd like to do is obtain is
a frequency count of the various occurrences of each probes
for each gene.
The data would look something like this:
Gene ProbeID
Expression_Level
A
1
0.34
A
2
0.21
E 3
0.11
A
4
0.21
F 5
0.56
F 6
0.87
.
.
.
(18 data points)
In each case, the probeID is unique. The output I am
looking for is something like this:
Gene No.ofprobes
Mean_expression
A
3
0.25
Is there an easy way to do this using cast or melt?
Ideally, I would also like to see the unique probes
corresponding to each gene in the wide format.
Thanks in advance
Max
Maxy Mariasegaram| Reserach Fellow | Australian Prostate
Cancer Research Centre| Level 1, Building 33 | Princess
Alexandra Hospital | 199 Ipswich Road, Brisbane QLD 4102
Australia | t: 07 3176 3073| f: 07 3176 7440 | e: maria...@qut.edu.au
[[alternative HTML version deleted]]
__
R-help@r-project.org
mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
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Re: [R] aggregating data
oops last reply was only half the solution:
library(plyr)
df - data.frame(gene=c('A', 'A', 'E', 'A', 'F', 'F'), probe = c(1,2,3,4,5,6),
exp = c(0.34, 0.21, 0.11, 0.21, 0.56, 0.81))
ddply(df, .(gene), function(df)c(length(df$gene), median(df$exp))
gene V1V2
1A 3 0.210
2E 1 0.110
3F 2 0.685
best
iain
--- On Thu, 30/6/11, Max Mariasegaram max.mariasega...@qut.edu.au wrote:
From: Max Mariasegaram max.mariasega...@qut.edu.au
Subject: [R] aggregating data
To: r-help@r-project.org r-help@r-project.org
Date: Thursday, 30 June, 2011, 8:28
Hi,
I am interested in using the cast function in R to perform
some aggregation. I did once manage to get it working, but
have now forgotten how I did this. So here is my dilemma. I
have several thousands of probes (about 180,000)
corresponding to each gene; what I'd like to do is obtain is
a frequency count of the various occurrences of each probes
for each gene.
The data would look something like this:
Gene ProbeID
Expression_Level
A
1
0.34
A
2
0.21
E 3
0.11
A
4
0.21
F 5
0.56
F 6
0.87
.
.
.
(18 data points)
In each case, the probeID is unique. The output I am
looking for is something like this:
Gene No.ofprobes
Mean_expression
A
3
0.25
Is there an easy way to do this using cast or melt?
Ideally, I would also like to see the unique probes
corresponding to each gene in the wide format.
Thanks in advance
Max
Maxy Mariasegaram| Reserach Fellow | Australian Prostate
Cancer Research Centre| Level 1, Building 33 | Princess
Alexandra Hospital | 199 Ipswich Road, Brisbane QLD 4102
Australia | t: 07 3176 3073| f: 07 3176 7440 | e: maria...@qut.edu.au
[[alternative HTML version deleted]]
__
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mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] median time period
Hello List
I'm trying to calculate the median period (in months) of a set of time
intervals (between two interventions).
I have been playing with the lubridate package to create the intervals but I
can't think of the right approach to get the median timeperiod.
Toy code:
library(lubridate)
test - c('08-04-22', '08-07-28', '09-03-02', '09-03-03', '09-01-30',
'09-03-09', '10-02-24', '10-03-05')
test - ymd(test)
intervals - as.period(test[5:8] - test[1:4])
intervals
[1] 9 months and 8 days7 months and 9 days11 months and 22 days
[4] 1 year and 2 days
How can I convert this 'period' object to months? From there I think I should
just convert to 'numeric' and calculate the median.
Garrett if you're out there - great package but could you help please!?
Best
iain
sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_0.2.4
loaded via a namespace (and not attached):
[1] plyr_1.5.2 stringr_0.4
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] median time period
Typical - you post to the list and then work it out for yourself!
Anyway here's my solution
Toy code as before then:
intervalsMonths - 12 * intervals$year + intervals$month
#convert whole years to months then add the remaining months for that entry in
intervals
medianMonths - median(as.numeric(intervalsMonths))
Best
iain
--- On Wed, 29/6/11, Iain Gallagher iaingallag...@btopenworld.com wrote:
From: Iain Gallagher iaingallag...@btopenworld.com
Subject: [R] median time period
To: r-help@r-project.org
Date: Wednesday, 29 June, 2011, 16:24
Hello List
I'm trying to calculate the median period (in months) of a
set of time intervals (between two interventions).
I have been playing with the lubridate package to create
the intervals but I can't think of the right approach to get
the median timeperiod.
Toy code:
library(lubridate)
test - c('08-04-22', '08-07-28', '09-03-02',
'09-03-03', '09-01-30', '09-03-09', '10-02-24', '10-03-05')
test - ymd(test)
intervals - as.period(test[5:8] - test[1:4])
intervals
[1] 9 months and 8 days 7 months and 9
days 11 months and 22 days
[4] 1 year and 2 days
How can I convert this 'period' object to months? From
there I think I should just convert to 'numeric' and
calculate the median.
Garrett if you're out there - great package but could you
help please!?
Best
iain
sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8
LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8
LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C
LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8
LC_NAME=C
[9] LC_ADDRESS=C
LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices
utils datasets
methods base
other attached packages:
[1] lubridate_0.2.4
loaded via a namespace (and not attached):
[1] plyr_1.5.2 stringr_0.4
__
R-help@r-project.org
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why doesn't this work ?
The first line of this reply is a definite candidate for the fortunes package! best i --- On Thu, 17/3/11, bill.venab...@csiro.au bill.venab...@csiro.au wrote: From: bill.venab...@csiro.au bill.venab...@csiro.au Subject: Re: [R] Why doesn't this work ? To: ericst...@aol.com, r-help@r-project.org Date: Thursday, 17 March, 2011, 3:54 It doesn't work (in R) because it is not written in R. It's written in some other language that looks a bit like R. t - 3 z - t %in% 1:3 z [1] TRUE t - 4 z - t %in% 1:3 z [1] FALSE -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of eric Sent: Thursday, 17 March 2011 1:26 PM To: r-help@r-project.org Subject: [R] Why doesn't this work ? Why doesn't this work and is there a better way ? z -ifelse(t==1 || 2 || 3, 1,0) t -3 z [1] 1 t -4 z [1] 1 trying to say ...if t == 1 or if t== 2 or if t ==3 then true, otherwise false -- View this message in context: http://r.789695.n4.nabble.com/Why-doesn-t-this-work-tp3383656p3383656.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Export R dataframes to excel
This appeared today on the r-bloggers site and might be useful for you.
http://www.r-bloggers.com/release-of-xlconnect-0-1-3/
cheers
i
--- On Tue, 1/3/11, Steve Taylor steve.tay...@aut.ac.nz wrote:
From: Steve Taylor steve.tay...@aut.ac.nz
Subject: Re: [R] Export R dataframes to excel
To: r-help@r-project.org, maxsilva mmsil...@uc.cl
Date: Tuesday, 1 March, 2011, 20:15
You can copy it with the following
function and then paste into Excel...
copy = function (df, buffer.kb=256) {
write.table(df,
file=paste(clipboard-,buffer.kb,sep=),
sep=\t, na='', quote=FALSE,
row.names=FALSE)
}
From: maxsilva mmsil...@uc.cl
To:r-help@r-project.org
Date: 2/Mar/2011 8:50a
Subject: [R] Export R dataframes to excel
I'm trying to do this in several ways but havent had any
result. Im asked to
install python, or perl etc. Can anybody suggest a
direct, easy and
understandable way? Every help would be appreciated.
Thx.
--
View this message in context:
http://r.789695.n4.nabble.com/Export-R-dataframes-to-excel-tp3330399p3330399.html
Sent from the R help mailing list archive at Nabble.com.
__
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mailing list
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PLEASE do read the posting guide http://www.R ( http://www.r/
)-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple plots using a loop
Hi Darcy
This works for me:
Factor - rep(factor(letters[1:4]), each = 10)
Size - runif(40) * 100
par(mfrow = c(2, 2))
for (i in unique(Factor)) {
hist(Size[Factor == i], main = i,
xlab = paste(n =,length(Size[Factor == i])), ylab = )
}
I think that using for (i in Factor) cycles through every occurrence of a level
and so you only get four plots of the last level rather than a plot for every
level.
cheers
iain
--- On Mon, 21/2/11, Darcy Webber darcy.web...@gmail.com wrote:
From: Darcy Webber darcy.web...@gmail.com
Subject: [R] multiple plots using a loop
To: r-help@r-project.org
Date: Monday, 21 February, 2011, 9:25
Dear R users,
I am trying to write myself a loop in order to produce a
set of 20
length frequency plots each pertaining to a factor level. I
would like
each of these plots to be available on the same figure, so
I have used
par(mfrow = c(4, 5)). However, when I run my loop below, it
produces
20 plots for each factor level and only displays the last
factor
levels LF plots. I'm fairly new to loops in R, so any help
would be
greatly appreciated.
I have provided an example data set below if required with
just 4
factors and adjusted par settings accordingly.
Factor - rep(factor(letters[1:4]), each = 10)
Size - runif(40) * 100
par(mfrow = c(2, 2))
for (i in Factor) {
LFchart - hist(Size[Factor == i], main = i,
xlab = c(n =,length(Size[Factor == i])), ylab = )
}
P.S. Also just a quick annoying question. My xlab
displays:
n =
120
I would like it to display:
n = 120
but just cant get it to work. Any thoughts.
Regar
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
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Re: [R] help with function
Ok - used browser to step through the function. Thanks for the nod towards that
Chuck.
tf2 - cumulMetric(tf1, deMirs$up)
Called from: cumulMetric(tf1, deMirs$up)
Browse[1] fcVector - as.numeric(with (deMirs, FC[match(deMirPresGenes[,4],
Probe)] ) )
Browse[1] metric - fcVector * as.numeric(deMirPresGenes[,11])
Browse[1] geneMetric - cbind(deMirPresGenes[,2], metric)
Browse[1] ls()
[1] deMirPresGenes deMirs fcVector geneMetric
[5] metric
Browse[1] listMetric - unstack(geneMetric,
as.numeric(geneMetric[,2])~geneMetric[,1])
Error in eval(expr, envir, enclos) : object 'geneMetric' not found
Browse[1] ls()
[1] deMirPresGenes deMirs fcVector geneMetric
[5] metric
Browse[1] head(geneMetric)
sym metric
[1,] AAK1 -0.35505
[2,] ABCA1 -0.34979
[3,] ABCA2 -1.0329
[4,] ABCB10 -1.22558
[5,] ABCE1 -0.61348
[6,] ABCF3 -0.86584
So geneMetric is there. It looks right but for some reason the call to unstack
cannot find it. Yet if I go through this line by line but not as a function the
call to unstack works fine:
fcVector - as.numeric(with (deMirs$up, FC[match(tf1[,4], Probe)] ) )
metric - fcVector * as.numeric(tf1[,11])
geneMetric - cbind(tf1[,2], metric)
head(geneMetric)
metric
[1,] AAK1 -0.35505
[2,] ABCA1 -0.34979
[3,] ABCA2 -1.0329
[4,] ABCB10 -1.22558
[5,] ABCE1 -0.61348
[6,] ABCF3 -0.86584
colnames(geneMetric) - c('sym', 'metric')
listMetric - unstack(geneMetric, as.numeric(geneMetric[,2])~geneMetric[,1])
head(listMetric)
$AAK1
[1] -0.35505
$ABCA1
[1] -0.34979
$ABCA2
[1] -1.0329
$ABCB10
[1] -1.22558
$ABCE1
[1] -0.61348
$ABCF3
[1] -0.86584
Any further advice would be much appreciated.
Thanks
i
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--- On Sat, 18/12/10, Charles C. Berry cbe...@tajo.ucsd.edu wrote:
From: Charles C. Berry cbe...@tajo.ucsd.edu
Subject: Re: [R] help with function
To: Iain Gallagher iaingallag...@btopenworld.com
Cc: r-help@r-project.org
Date: Saturday, 18 December, 2010, 0:13
On Fri, 17 Dec 2010, Iain Gallagher
wrote:
Hello List
I'm moving this over from the bioC list as, although
the problem I'm working on is biological, the current bottle
neck is my poor understanding of R.
I wonder if someone would help me with the following
function.
Here is how I'd take it apart.
Either
1) put browser() as the first line of the
function,then feed lines to the
browser one -by-one to see where
it hangs,
2) trace(cumulMetric) , then try to run it (much
like 1, but it will
handle feeding the lines of the
function more easily)
3) options( error = recover ), then run it till it
hits the error, then
browser thru the frames to see
what is where
See
?browser
?trace
?recover
as background.
HTH,
Chuck
cumulMetric - function(deMirPresGenes, deMirs){
#need to match position of each miR in deMirPresGenes
with its FC to form a vector of FC in correct order
fc - deMirs
fcVector - as.numeric(with (fc,
FC[match(deMirPresGenes[,4], Probe)] ) )
#multiply fc by context score for each
interaction
metric - fcVector *
as.numeric(deMirPresGenes[,11])
geneMetric - cbind(deMirPresGenes[,2],
as.numeric(metric))
#make cumul weighted score
listMetric - unstack(geneMetric,
as.numeric(geneMetric[,2])~geneMetric[,1])
listMetric -
as.data.frame(sapply(listMetric,sum)) #returns a dataframe
colnames(listMetric) - c('cumulMetric')
#return whole list
return(listMetric)
}
deMirPresGenes looks like this:
Gene.ID Gene.Symbol Species.ID miRNA
Site.type UTR_start UTR_end
X3pairing_contr local_AU_contr position_contr
context_score context_percentile
22848 AAK1 9606 hsa-miR-183 2
1546 1552 -0.026 -0.047 0.099
-0.135 47
19 ABCA1 9606 hsa-miR-183 2
1366 1372 -0.011 -0.048 0.087
-0.133 46
20 ABCA2 9606 hsa-miR-495 2
666 672 -0.042 -0.092 -0.035
-0.33 93
23456 ABCB10 9606 hsa-miR-183 3
1475 1481 0.003 -0.109 -0.05
-0.466 98
6059 ABCE1 9606 hsa-miR-495 2
1474 1480 0.005 -0.046 0.006
-0.196 58
55324 ABCF3 9606 hsa-miR-1275 3
90 96 0.007 0.042 -0.055
-0.316 94
although it is much longer in 'real
Re: [R] [BioC] problem with function
Hi Christian, Chuck (and lists)
It seems that the problem may be the strange behaviour of 'unstack' inside a
function.
See this thread in the R mailing list:
http://tolstoy.newcastle.edu.au/R/help/04/03/1160.html
Anyway, I got round the problem by using 'aggregate' instead of converting to a
list and then tapply to sum values of metric. Probably more efficient as well.
Thanks for the help offered.
My function now looks like this (for the record!) and behaves as it should.
makeMetric - function(deMirPresGenes, deMirs){
#need to match position of each miR in deMirPresGenes with its FC to form a
vector of FC in correct order
fcVector - as.numeric(with (deMirs, FC[match(deMirPresGenes[,4], Probe)] )
)
#multiply fc by context score for each interaction
metric - fcVector * as.numeric(deMirPresGenes[,11])
geneMetric - cbind(deMirPresGenes[,2], metric)
colnames(geneMetric) - c('sym', 'metric')
#make cumul by aggregate
listMetric - aggregate(as.numeric(geneMetric[,2]), list(geneMetric[,1]),
sum)#returns a dataframe
colnames(listMetric) - c('symbol','cumulMetric')
#return whole list
return(listMetric)# dataframe
}
Cheers
i
--- On Sat, 18/12/10, cstrato cstr...@aon.at wrote:
From: cstrato cstr...@aon.at
Subject: Re: [BioC] problem with function
To: Iain Gallagher iaingallag...@btopenworld.com
Cc: bioconductor bioconduc...@stat.math.ethz.ch
Date: Saturday, 18 December, 2010, 14:40
You need to do:
cumulMetric - function(deMirPresGenes, deMirs){
fc - deMirs
fcVector - as.numeric(with (fc,
FC[match(deMirPresGenes[,4], Probe)] ) )
metric - fcVector *
as.numeric(deMirPresGenes[,11])
geneMetric -
as.data.frame(cbind(deMirPresGenes[,2],
as.numeric(metric)))
colnames(geneMetric) - c('y', 'x')
listMetric - unstack(geneMetric, x ~
y)
listMetric -
as.data.frame(sapply(listMetric,sum)) #returns a dataframe
colnames(listMetric) -
c('cumulMetric')
return(listMetric)
}
Regards
Christian
On 12/17/10 11:52 PM, Iain Gallagher wrote:
ok... done. Not really any further forward here.
print statements after creating fcVector, metric and
geneMetric (see output below). They all look ok in terms of
structure and length. But the error persists and listMetric
is not made?!?! Odd.
I have added some comments to the output below.
tf2-cumulMetric(tf1, deMirs$up)#deMirs$up is a
dataframe (see prev posts)
[1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector -
looks ok
[1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348
-0.86584 # print metric - looks ok
[1] 1045 # lengthof metric - is correct
sym
metric # print geneMetric - looks ok
[1,] AAK1 -0.35505
[2,] ABCA1 -0.34979
[3,] ABCA2 -1.0329
[4,] ABCB10 -1.22558
[5,] ABCE1 -0.61348
[6,] ABCF3 -0.86584
[1] 1045 # nrow of geneMetric - is correct
Error in eval(expr, envir, enclos) : object
'geneMetric' not found
cheers
i
--- On Fri, 17/12/10, cstratocstr...@aon.at
wrote:
From: cstratocstr...@aon.at
Subject: Re: [BioC] problem with function
To: Iain Gallagheriaingallag...@btopenworld.com
Cc: bioconductorbioconduc...@stat.math.ethz.ch
Date: Friday, 17 December, 2010, 22:38
At the moment I have no idea, but
what I would do in this case is to put
print() statements after each line to see where it
fails.
Christian
On 12/17/10 10:59 PM, Iain Gallagher wrote:
Hi
FC is the second column of the deMirs
variable. deMirs
is a dataframe with 2 columns - Probe (e.g.
hsa-miR-145) and
FC (e.g 1.45). Using 'with' allows me to use
deMirs as an
'environment'. I thus don't have to pass FC
explicitly.
Cheers
i
--- On Fri, 17/12/10, cstratocstr...@aon.at
wrote:
From: cstratocstr...@aon.at
Subject: Re: [BioC] problem with function
To: Iain Gallagheriaingallag...@btopenworld.com
Cc: bioconductorbioconduc...@stat.math.ethz.ch
Date: Friday, 17 December, 2010, 20:39
What is FC[]? It is not passed
to the function. Christan
On 12/17/10 8:11 PM, Iain Gallagher
wrote:
Sorry.
That was a typo. In my script
deMirPresGenes1[,4] is
deMirPresGenes[,4].
Just to be sure I'm going about this
the right
way
though I should say that at the moment I
assign
the output
of another function to a variable called
'tf1' -
this object
is the same as the deMirPresGenes is my
previous
email.
This is then fed to my problem
function using
positional matching.
e.g. tf2- cumulMetric(tf1,
deMirs)
Which leads to:
Error in eval(expr, envir, enclos) :
object
'geneMetric' not found
Hey ho!
i
--- On Fri, 17/12/10, cstratocstr...@aon.at
wrote:
From: cstratocstr...@aon.at
Subject: Re: [BioC] problem with
function
To: Iain Gallagheriaingallag...@btopenworld.com
Cc: bioconductorbioconduc...@stat.math.ethz.ch
Date: Friday, 17 December, 2010,
18:40
I am not sure but I would say
[R] help with function
Hello List
I'm moving this over from the bioC list as, although the problem I'm working on
is biological, the current bottle neck is my poor understanding of R.
I wonder if someone would help me with the following function.
cumulMetric - function(deMirPresGenes, deMirs){
#need to match position of each miR in deMirPresGenes with its FC to form a
vector of FC in correct order
fc - deMirs
fcVector - as.numeric(with (fc, FC[match(deMirPresGenes[,4], Probe)] ) )
#multiply fc by context score for each interaction
metric - fcVector * as.numeric(deMirPresGenes[,11])
geneMetric - cbind(deMirPresGenes[,2], as.numeric(metric))
#make cumul weighted score
listMetric - unstack(geneMetric, as.numeric(geneMetric[,2])~geneMetric[,1])
listMetric - as.data.frame(sapply(listMetric,sum)) #returns a dataframe
colnames(listMetric) - c('cumulMetric')
#return whole list
return(listMetric)
}
deMirPresGenes looks like this:
Gene.ID Gene.Symbol Species.ID miRNA Site.type UTR_start
UTR_end X3pairing_contr local_AU_contr position_contr
context_score context_percentile
22848 AAK1 9606 hsa-miR-183 2 1546 1552 -0.026 -0.047
0.099 -0.135 47
19 ABCA1 9606 hsa-miR-183 2 1366 1372 -0.011 -0.048
0.087 -0.133 46
20 ABCA2 9606 hsa-miR-495 2 666 672 -0.042 -0.092
-0.035 -0.33 93
23456 ABCB10 9606 hsa-miR-183 3 1475 1481 0.003 -0.109
-0.05 -0.466 98
6059 ABCE1 9606 hsa-miR-495 2 1474 1480 0.005 -0.046
0.006 -0.196 58
55324 ABCF3 9606 hsa-miR-1275 3 90 96 0.007 0.042
-0.055 -0.316 94
although it is much longer in 'real life'.
The aim of the function is to extract a dataframe of gene symbols along with a
weighted score from the above data. The weighted score is the FC column of
deMirs * the context_score column of deMirPresGenes. This is easy peasy!
Where I'm falling down is that if I run this function it complains that
'geneMetric' can't be found. Hmm - I've run it all line by line (i.e. not as a
function) and it works but wrapped up like this it fails!
e.g.
testF2 - cumulMetric(testF1, deMirs$up)
Error in eval(expr, envir, enclos) : object 'geneMetric' not found
deMirs$up looks like this:
Probe FC
hsa-miR-183 2.63
hsa-miR-1275 2.74
hsa-miR-495 3.13
hsa-miR-886-3p 3.73
hsa-miR-886-5p 3.97
hsa-miR-144* 6.62
hsa-miR-451 7.94
In an effort to debug this I have examined each object using 'print' statements
(as suggested by cstrato on the bioC list).
All the objects in the function up until listMetric look ok in terms of
structure and length. But the error persists and listMetric is not made?!?! Odd.
I have added some comments to the output below.
tf2-cumulMetric(tf1, deMirs$up)#deMirs$up is a dataframe (see above - it is
the same as deMirs)
[1] 2.63 2.63 3.13 2.63 3.13 2.74 # print fcVector - looks ok
[1] -0.35505 -0.34979 -1.03290 -1.22558 -0.61348 -0.86584 # print metric -
looks ok
[1] 1045 # length of metric - is correct
sym metric # print geneMetric - looks ok
[1,] AAK1 -0.35505
[2,] ABCA1 -0.34979
[3,] ABCA2 -1.0329
[4,] ABCB10 -1.22558
[5,] ABCE1 -0.61348
[6,] ABCF3 -0.86584
[1] 1045 # nrow of geneMetric - is correct
Error in eval(expr, envir, enclos) : object 'geneMetric' not found
Could someone possibly point out where I falling down.
Thanks
iain
sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.12.0
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] where do I send typos?
Best to send any comments on documentation to the author of the documentation. iain --- On Fri, 26/3/10, Xu Wang xuwang...@gmail.com wrote: From: Xu Wang xuwang...@gmail.com Subject: [R] where do I send typos? To: r-help@r-project.org Date: Friday, 26 March, 2010, 5:15 Hi, I notice several typos when reading documentation and I verify that they are still typos in the current build. Where do I send corrections? Note that most of them are minor typos. Thanks -- View this message in context: http://n4.nabble.com/where-do-I-send-typos-tp1691713p1691713.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] netlabR package in English
Keith Download the netLabR package from http://www.meduniwien.ac.at/user/georg.dorffner/netalg.html i.e. download the .tar.gz or zip files. Inside these, in the inst/doc directory you'll find two English manuals. HTH iain --- On Thu, 25/3/10, Keith McMillan keith.mcmil...@merrickbank.com wrote: From: Keith McMillan keith.mcmil...@merrickbank.com Subject: [R] netlabR package in English To: r-help@r-project.org Date: Thursday, 25 March, 2010, 21:24 Dear R users, Is documentation for the netlabR package available in English? If not does anyone know if or when it will be? Regards, Keith This e-mail and any files transmitted with it are confidential and are intended solely for the use of the individual or entity to whom it is addressed. If you are not the intended recipient or the person responsible for delivering the e-mail to the intended recipient, be advised that you have received this e-mail in error, and that any use, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. If you received this e-mail in error, please return the e-mail to the sender at Merrick Bank and delete it from your computer. Although Merrick Bank attempts to sweep e-mail and attachments for viruses, it does not guarantee that either are virus-free and accepts no liability for any damage sustained as a result of viruses. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] logical operations with lists
a-list('a', 'b', 'c')
b-list('c', 'd', 'e')
c-intersect(a,b)
c
[[1]]
[1] c
Is this what you want?
Cheers
Iain
--- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov
wrote:
From: Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov
Subject: [R] logical operations with lists
To: r-help@r-project.org r-help@r-project.org
Date: Friday, 12 February, 2010, 22:06
Sorry, maybe it's easy but I haven't
found anything useful:
how can I obtain a list C that contains all the members in
the list B that are not in list A? This are lists of nanes,
not numbers!
Thank you
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and
Hematology, University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppo...@mail.nih.gov
__
R-help@r-project.org
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] logical operations with lists
sorry, misread your post try this... c-setdiff(a,b) c [[1]] [1] a [[2]] [1] b for a list C that contains all the members in the list B that are not in list A --- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov wrote: From: Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov Subject: [R] logical operations with lists To: r-help@r-project.org r-help@r-project.org Date: Friday, 12 February, 2010, 22:06 Sorry, maybe it's easy but I haven't found anything useful: how can I obtain a list C that contains all the members in the list B that are not in list A? This are lists of nanes, not numbers! Thank you Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] logical operations with lists
these are vectors in R not lists
try:
a-c('a', 'b', 'c')#first vector (like A)
a
[1] a b c
b-c('c', 'd', 'e')#second vector (like B)
b
[1] c d e
c-setdiff(b,a)# all those in B but not A
c
[1] d e
cheers
iain
--- On Fri, 12/2/10, Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov
wrote:
From: Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov
Subject: Re: [R] logical operations with lists
To: r-help@r-project.org r-help@r-project.org
Date: Friday, 12 February, 2010, 22:57
I'm sorry but here's what I get:
A[1:10,]
[1] UQCRC1 IDH3B PDHA1 SUCLA2 COX5B
SDHB SDHA MDH2 DLD
COQ7
dim(A)
[1] 1013 1
B[1:10,]
[1] 3.8-1.2 3.8-1.3 3.8-1.4 3.8-1.5 5-HT3c2 A1BG
A1CF
A2BP1 A2LD1 A2M
dim(B)
[1] 55546 1
C-rbind(A,B)
dim(C)
[1] 56559 1
D - C[which(C %in% A ==FALSE)]
dim(D)
[1] 56559 0
and so with any other proposed method.
I imported the list A and B this way:
A-as.vector(read.delim(E:/A.txt,sep=\t,header=FALSE))
and then removed the redundant rows with:
A-unique(A)
Guess I'm doing something really wrong here... Sorry for
the inexperience, I'm trying to improve...
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and
Hematology, University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppo...@mail.nih.gov
From: jbreic...@gmail.com
[jbreic...@gmail.com]
On Behalf Of Jonathan [jonsle...@gmail.com]
Sent: Friday, February 12, 2010 5:21 PM
To: Zoppoli, Gabriele (NIH/NCI) [G]
Cc: r-help@r-project.org
Subject: Re: [R] logical operations with lists
This is probably not the best way, but (assuming you had
vectors and
not lists, since I'm not sure what your list looks like):
C - B[which(B %in% A ==FALSE)]
Regards,
Jonathan
On Fri, Feb 12, 2010 at 5:06 PM, Zoppoli, Gabriele
(NIH/NCI) [G]
zoppo...@mail.nih.gov
wrote:
Sorry, maybe it's easy but I haven't found anything
useful:
how can I obtain a list C that contains all the
members in the list B that are not in list A? This are lists
of nanes, not numbers!
Thank you
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and
Hematology, University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppo...@mail.nih.gov
__
R-help@r-project.org
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
R-help@r-project.org
mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Upgrading To 2.10 from 2.6.2
Hi Steve Have you tried: apt-cache search gfortran in a terminal window. Then sudo apt-get install theRelevantPackage I think you also need the Universe repos enabled. HTH Iain --- On Tue, 8/12/09, steve_fried...@nps.gov steve_fried...@nps.gov wrote: From: steve_fried...@nps.gov steve_fried...@nps.gov Subject: [R] Upgrading To 2.10 from 2.6.2 To: r-help@r-project.org Date: Tuesday, 8 December, 2009, 13:38 Hello I have a Linux machine (Ubuntu 8.04 hardy, Gcc version 4.2.4 (i486-linux-gnu) currently running R 2.6.2. I'd like to upgrade to 2.10. First Question): What is the appropriate way to remove the old version of R? Part 2. After downloading r-base_2.10.0.orig.tar.gz and opening the archive. I ran the ./configure routine. It failed claiming that it could not find the F77 compiler. My sys admin and I searched for a compiler, but have not succeeded in finding one compatible for Ubuntu 8.04. 2nd Question: Would you be so kind and point me towards one? Thanks in advance Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] string splitting and testing for enrichment
Hi List I have data in the following form: Gene TFBS NUDC PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191) RPA2 STAT4(57) HEB(251) TAF12 PAX3(53) YY1(92) BRCA(99) GLI(101) EIF3I NERF(10) P300(10) TRAPPC3 HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122) TRAPPC3 EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121) ZTA(168) NDUFS5 WHN(14) ATF(57) EGR3(59) PAX5(99) SF1(108) NRSE(146) TIE1 NRSE(129) I would like to test the 2nd column (each value has letters followed by numbers in brackets) here for enrichment via fisher.test. To that end I am trying to create two factors made up of column 1 (Gene) and column 2 (TFBS) where each Gene would have several entries matching each TFBS. My main problem just now is that I can't split the TFBS column into separate strings (at the moment that 2nd column is all one string for each Gene). Here's where I am just now: test-as.character(dataIn[,2]) # convert the 2nd column from factor to character test2-unlist(strsplit(test[1], ' ')) # split the first element into individual strings (only the first element just now because I'm joust trying to get things working) test3-unlist(strsplit(test2, '\\([0-9]\\)')) # get rid of numbers and brackets now this does not behave as I hoped - it gives me: test3 [1] PPARA HNF4(20) HNF4(96) [4] AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) [7] HLF(191) ie it only removes the numbers and brackets from the first entry and not the others. Could someone point out my mistake please? Once I have all the TFBS (letters only) for each Gene I would then count how often a TFBS occurs and use this data for a fisher.test testing for enrichment of TFBS in the list I have. I'm a rather muddled here though and would appreciate advice on whether this is the right approach. Thanks Iain sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] arithmetic problem
Hello list I have a problem with a dataset (see toy example below) where I am trying to find the difference between two (or more numbers) and discard those observations which fall outside a set interval. An example and further explanation: values ind 12655 7A5 23028 7A5 3 689 ABBA-1 41336 ABBA-1 51560 ABBA-1 62820 ABLIM1 73339 ABLIM1 8 171ACSM5 9 195ACSM5 10 43 ADAMDEC1 11129 ADAMDEC1 12 1105 AFF1 13 3202 AFF1 14852 AFF3 15 2461 AFF3 16 45 AKT1 17397 AKT1 18 1430 AQP2 19 2402 AQP2 20 2551 ARHGAP19 Each number in the values column above is associated with a label (in the ind column). For some inds there will be only 2 values but as can be seen from the data other inds have many values. Here's what I want to do using the ABBA-1 data from above as an example: calculate the differences between each value: 1560-1336 = 224 1336-689 = 647 then use these values to create an index that will allow me to pull out values between set limits. If I set the limits to between 200 and 300 then the index will reference rows 4 5 in the above data set. I hope this is reasonably clear and I appreciate any suggestions. Thanks Iain __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] counting occurrence of text in a dataframe
Hello list. I am hoping for some help with a relatively simple problem. I have a data frame arranged as below. I want to be able to count the occurrence of each gene (eg let-7e) by Experiment. In other words how many times does a given gene crop up in the dataframe. I tried table but couldn't work out how to get the output I want. I have also considered rearranging this data into a list (by gene) and then counting the length of each gene element. However I thought that there might be a more elegant solution. Tanaka Mitchell Wang Hunter Chen Chim miR-191* let-7e let-7b miR-126let-7a let-7g miR-198let-7f let-7c miR-146a let-7b let-7i miR-22 let-7g miR-1224 miR-16 let-7d miR-130b miR-223let-7i miR-124miR-191let-7f miR-133a miR-296let7fG15A miR-125a-3pmiR-222let-7g miR-140 miR-30dmiR-101miR-125b-5pmiR-223let-7i miR-142-5p miR-370miR-103miR-133a miR-24 miR-101miR-146 miR-486miR-125a-5pmiR-133b miR-26amiR-103miR-148a miR-498miR-126miR-135a* miR-32 miR-106a miR-152 Thanks for any advice. Cheers Iain __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] replacing values in a vector
Hello list.
I have a vector of values:
eg
head(diff_mirs_list)
[1] hsa-miR-26b hsa-miR-26b hsa-miR-23a hsa-miR-27b hsa-miR-29a
[6] hsa-miR-29b
and I would like to conditionally replace each value in this vector with a
number defined in a dataframe:
fc
Probe ave.fc
1 hsa-let-7a 1.28
2 hsa-miR-100 1.47
3 hsa-miR-125a-5p 1.31
4 hsa-miR-140-3p 1.28
5 hsa-miR-143 1.98
6 hsa-miR-193a-3p 1.37
7 hsa-miR-193b 1.48
8 hsa-miR-195 1.16
9 hsa-miR-214 1.22
10 hsa-miR-23a 1.21
11 hsa-miR-26b 1.13
12 hsa-miR-27b 1.37
13 hsa-miR-29a 1.24
14 hsa-miR-29b 1.69
15 hsa-miR-30b 1.16
16 hsa-miR-424 1.42
17 hsa-miR-768-3p 1.48
18 hsa-miR-886-3p 1.43
19 hsa-miR-933 1.23
ie every hsa-let-7a in the diff_mirs_list is replaced by 1.28, hsa-miR-100 by
1.47 etc etc
I have tried to make a loop to use gsub eg
for (i in 1:nrow(fc)){
+ test-gsub(fc[i,1], fc[i,2], diff_mirs_list)
}
but this obviously passes the unchanged vector to gsub each time and so I get
back my 'test' vector with only hsa-miR-933 changed. Could someone help me out
with this please.
Thanks
Iain
sessionInfo()
R version 2.8.0 (2008-10-20)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Free SQL Database with R
Hi Chibisi I'm sort of jumping into this thread but from your description of charts / plotting below I thought you might like to take a look at flot: http://code.google.com/p/flot/ From the page Flot is a pure Javascript plotting library for jQuery. It produces graphical plots of arbitrary datasets on-the-fly client-side. The focus is on simple usage (all settings are optional), attractive looks and interactive features like zooming. Although Flot is easy to use, it is also advanced enough to be suitable for Web 2.0 data mining/business intelligence purposes which is its original application. The plugin is targeting all newer browsers. If you find a problem, please report it. Drawing is done with the canvas tag introduced by Safari and now available on all major browsers, except Internet Explorer where the excanvas Javascript emulation helper is used. Maybe it could be useful to you for plots etc. Cheers Iain Chibisi Chima-Okereke [EMAIL PROTECTED] wrote: Dear Felix, Thanks for the reply, If you haven't already guessed I am new to web programming. The sort of webpage I want to build is one that presents quantitative information in graphs and charts, that people can interact with, e.g. select parts of charts to zoom into, highlight values, click buttons to do analysis on the data displayed, so yes some sort of interactive GUI. I initially thought of using flash as a front end but I don't know any actionscript, so learning that would to a suitable standard take alot of extra time, and I think it would be best if everything could be done in R as much as possible. If I used an RGUI I guess I would be using the playwith package? Do the consumers of the website need to have R to consume stuff displayed with an RGUI? The database itself would just be pretty static just being queried for information, unless some analysis was required in which case R would query the database do the analysis and write the analysis back to the database (I guessing that is the way it would be done), before it gets displayed on the web page. Kind Regards Chibisi On Wed, Sep 3, 2008 at 11:39 AM, drflxms wrote: Hello Chibisi, I am not shore whether I completely understand your needs: Do you want to build a webpage which relies on a content management system (cms)? Do you want to collect data (i.e. survey) which later on shall be analysed using R? Or shall it be a webpage with an interactive R GUI? What else? But personally I would prefer MySQL as backend for websites, as most professional (opensource) cms (i.e. typo3, wordpress etc.) are created with MySQL in mind. There is a good interface between R and MySQL called RMySQL as well. I use this on a daily basis, as all my data is stored in a local MySQL database (more flexible than always reading in text files - at least in my opinion). Hope this personal view might help a little bit. Cheers, Felix __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with data layout
Hello list I have been given some Excel sheets with data laid like this: Col1Col2 A 3 2 3 B 4 5 4 C 1 4 3 I was hoping to import this into R as a csv and then get the mean and SD for each letter in column 1. Could someone give me some guidance on best to approach this? Thanks Iain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with data layout - Thanks
Thanks for all the excellent replies. Iain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Another failed attempt to install an R package in Ubuntu
Hi Miklos. If you want to install R packages to the /usr/lib/R/library directory you need to start R with 'root' user privileges. Ordinary users do not have the appropriate permissions to write to this directory. At the command line type: sudo R type your password when prompted. You won't need to do this for using R or the packages though; you can start R with you normal user permissions ie in the usual way. There are many online tutorials for the linux permission system... have a google ;-) Your error messages suggest you missing some header files (eg stdlib.h is the header file for the general purpose C library) used to build code. At the command line try this: sudo apt-get install build-essentials That will install many of the files you need. There are many apt-get primers on the web as well; it's worth having a look. Hope this helps somewhat. Cheers Iain Miklos Kiss [EMAIL PROTECTED] wrote: I am running Ubuntu 8.04 through Wubi on a HP Pavilion dv4000 (my home computer) and I recently installed R 2.7.1. I attempted to install the randomForest package from within the R environment and from the Linux terminal. Both attempts failed. I've tried several mirrors but with no luck. Below is an example of the series of error messages I got when R told me that the installation wasn't going well. It tells me that several header files are missing. For some reason it is also trying to install them in '/home/mik/R/i486-pc-linux-gnu-library/2.7' but my R library packages are located in '/usr/lib/R/library'. I tried downloading various x11dev packages and such, as suggested in similar threads in this forum, but that didn't seem to help. I'm really new (installed Ubuntu less than 4 months ago) to Linux but I've been using R for about a year. If anyone can point me in the right direction on how to correctly install this package, I'd very much appreciate it. Thank you, Miklos Kiss install.packages() --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done Warning in install.packages() : argument 'lib' is missing: using '/home/mik/R/i486-pc-linux-gnu-library/2.7' trying URL 'http://cran.mtu.edu/src/contrib/randomForest_4.5-25.tar.gz' Content type 'application/x-gzip' length 70212 bytes (68 Kb) opened URL == downloaded 68 Kb * Installing *source* package 'randomForest' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c classTree.c -o classTree.o In file included from classTree.c:15: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory In file included from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:7, from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:11, from /usr/share/R/include/R.h:30, from classTree.c:15: /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:122:61: error: limits.h: No such file or directory In file included from classTree.c:15: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from classTree.c:15: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory classTree.c: In function âcatmax_â: classTree.c:305: warning: implicit declaration of function âpowâ classTree.c:305: warning: incompatible implicit declaration of built-in function âpowâ make: *** [classTree.o] Error 1 ERROR: compilation failed for package 'randomForest' ** Removing '/home/mik/R/i486-pc-linux-gnu-library/2.7/randomForest' The downloaded packages are in /tmp/RtmpT83A76/downloaded_packages Warning message: In install.packages() : installation of package 'randomForest' had non-zero exit status -- View this message in context: http://www.nabble.com/Another-failed-attempt-to-install-an-R-package-in-Ubuntu-tp18415721p18415721.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] txt file, 14000+ rows, only last 8000 appear
I'm pretty sure I've had similar problems to this in the past and the problem has been a badly formatted text file ie you think it's all tab delimited but it's not. I can't be more specific (because it's your file) but it would be worth copying the non appearing rows into a separate file and see if you can track down the region of the file that's causing the problem. Cheers Iain RobertsLRRI [EMAIL PROTECTED] wrote: You are asked to follow the posting guide and to provide commented, minimal, self-contained, reproducible code. Code entered: Influenza-read.delim(C://Documents and Settings//rroberts//desktop//H5N1//0v8a1n3.dat.txt) Influenza rows 6505 ... 14421 So the first 6504 rows aren't displayed Thank you -- View this message in context: http://www.nabble.com/txt-file%2C-14000%2B-rows%2C-only-last-8000-appear-tp17701519p17735926.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
