, Michael Dewey ()
escribió:
> Dear Ana
>
> When you installed R it gave you an option to put a shortcut on the
> desktop. If you did that then you can start the R GUI by clicking on it.
> You may need to customise it for your preferences. Specifically it
> starts R with an option cd
Hello,
I am sorry for my ignorance, but what is Rgui.exe?
El mar, 21 nov 2023 a las 12:06, Ivan Krylov ()
escribió:
> В Tue, 21 Nov 2023 10:51:59 +0100
> Ana de las Heras Molina пишет:
>
> > I uninstalled onedrive, I eliminated all the folders and then
> > rein
Hi,
I uninstalled onedrive, I eliminated all the folders and then reinstalled R
and RStudio... but it is RStudio the one creating a folder
called C:\Users\Ana\OneDrive - Universidad Complutense de Madrid
(UCM)\Documentos.
This is what I obtained with the debugging
Error in setwd(dir) : no es
Hello,
Thank you all for your responses. When I initialize R, the folder in which
it starts is:
getwd()
[1] "C:/Users/Ana/OneDrive - Universidad Complutense de Madrid
(UCM)/Documentos"
So it seems a problem with OneDrive
-Kevin: I do not really understand your question... You mean i
Hello,
I am Ana de las Heras, and I write to you because every time I open RStudio
or R directly I have the following message, before I can do anything at
all:
Error in setwd(dir) : no es posible cambiar el directorio de trabajo
At first I didn't pay much attention to it, but I am having lots
I have code like this:
data <- read.csv("test1.csv", stringsAsFactors=FALSE, header=TRUE)
# Graph
myplot=ggplot(data, aes(fill=condition, y=value, x=condition)) +
geom_bar(position="dodge", stat="identity", width=0.5) +
scale_fill_manual(values=c("#7b3294", "#c2a5cf", "#a6dba0",
", "18.7", "19", "6.4", "8.4", "20", "20.6"), PIE.3D.FFT = c("6",
"8.6", "5.7", "4.3", "1 .0", "1 .1", "7.6", "8.4"), PIE.3D.FFT.comm. = c
orical data, but not continuous, numeric data which are better
> handled with box plots or strip charts.
>
> Do not use printouts of your data since it hides important information.
> Use str(a11) and dput(a11) or dput(head(a11)) to provide useful information
> about your data.
>
>
end= rownames(data2), beside=
TRUE,las=2,cex.axis=0.7,cex.names=0.7,ylim=c(0,80), col=c("#9e9ac8",
"#6a51a3"))
If I don't log transform my code runs.
Please advise,
Ana
[[alternative HTML version deleted]]
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trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Thu, Oct 14, 2021 at 10:10 AM Ana Marija
> wrote:
>
>> Hi All,
>>
>> I hav
uct of natural log. I have to do
inverse of it.
So for example do do inverse of 0.6931472 I would do:
> 2.718281828^0.6931472
[1] 2
How do I perform this operation for every single value in this data frame?
The original data frame is this dimension:
> dim(b)
[1] 1441 18
T
gt; -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Fri, Sep 17, 2021 at 12:22 PM Ana Marija
> wrote:
> >
> > Hi All,
> >
> > I plan to identify metabolite levels that differ between individuals
> > with various retinopa
.
Can you please help,
Thanks
Ana
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and provide commented
)
> #[1] 145092258
>
> df[14509227,] # beyond nrow(df) by 2
>
>
> Hope this helps,
>
> Rui Barradas
>
>
> Às 15:12 de 16/09/21, Ana Marija escreveu:
> > Hi All,
> >
> > I have lines in file that look like this:
> >
> >> df[14
N
"numeric" "integer"
> dim(df)
[1] 145092258
Tried:
> df=na.omit(df)
> dim(df)
[1] 145092258
and:
> library(tidyr)
> d=df %>% drop_na()
> dim(d)
[1] 145092258
Please advise,
Thanks
Ana
___
ec[df1]
oavec<-tausqvec*avec
buw<-sum(oavec*beta1vec)/sum(oavec)
lamvec<-cvec*sum(oavec*(beta1vec-buw)^2)/sigsq
ep<-ep+sum(wcpdf*pf(fcrit,df1,df,lamvec,lower.tail=FALSE))
}
kbpower<-ep/repn
}
kbpower<-kbpowerf()
for minfi package including making MDS plots:
https://www.bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html
Thanks
Ana
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rsplit(names, ":")[-2]]
out <- data[, .(rsid, ref_allele, eff_allele)][,
WGT := files[i]][]
}
return(out)
rm(data)
gc()
}
parallel::stopCluster(cl)
big_data <- rbindlist(lst_out, fill = TRUE)
On Wed, Dec 16, 2020 at 9:31 AM Ana Marija wrote:
>
ster(cl)
big_data <- rbindlist(lst_out)
and i got:
Error in { : task 4 failed - "$ operator is invalid for atomic vectors"
> parallel::stopCluster(cl)
I uploaded 3 RDat file here if you want to try it
https://github.com/montenegrina/sample
Thank you for looking into this
Ana
On Tue, D
names(a)
data <- data.table(names, a["blup"])
nm1 <- c("rsid", "ref_allele", "eff_allele")
any idea how I can rewrite this?
On Tue, Dec 15, 2020 at 8:30 PM Jim Lemon wrote:
>
> Hi Ana,
> I would look at "data" in your second example
parallelized version.
On Tue, Dec 15, 2020 at 7:35 PM Jim Lemon wrote:
>
> Hi Ana,
> My guess is that in your second code fragment you are assigning the
> rownames of "a" and the _values_ contained in a$blup to the data.table
> "data". As I don't have
quot;, "eff_allele")
data[, (nm1) := tstrsplit(names, ":")[-2]]
return(data[, .(rsid, weight = blup, ref_allele, eff_allele)][,
WGT := files[i]][])
}
parallel::stopCluster(cl)
big_data <- rbindlist(lst_out)
I am getting this Error:
Error in { : t
lp page, ?corrplot .
>
> --
>
> David.
>
> On 11/6/20 6:08 AM, Ana Marija wrote:
>
> sorry forgot to attach the plot.
>
> On Fri, Nov 6, 2020 at 8:07 AM Ana Marija wrote:
>
> Hello
>
> I have data like this:
>
> head(my_data)
>
> subjects DIABDUR HB
sorry forgot to attach the plot.
On Fri, Nov 6, 2020 at 8:07 AM Ana Marija wrote:
>
> Hello
>
> I have data like this:
>
> > head(my_data)
> subjects DIABDUR HBA1C ESRD SEX AGE PHENO C1 C2
> 1 fam0110_G110 38 9.41 2 51 2 -
uot;correlation.pdf")
corrplot(res, type = "upper", order = "hclust",
tl.col = "black", tl.srt = 45)
dev.off()
and I am getting the plot in attach. How to make it so that my
variables are shown on the plot in the order they are in my_data data
frame?
Th
Makes sense, thank you!
On Wed, 21 Oct 2020 at 17:46, Rolf Turner wrote:
>
> On Wed, 21 Oct 2020 16:15:22 -0500
> Ana Marija wrote:
>
> > Hello,
> >
> > I have a data frame with one column:
> >
> > > remove
> >
> >
e %in% as.character(remove$V1)]
> >
> >
> > Hope this helps,
> >
> > Rui Barradas
> >
> > Às 22:15 de 21/10/20, Ana Marija escreveu:
> >> Hello,
> >>
> >> I have a data frame with one column:
> >>
&g
ied doing this:
b= celFiles[!basename(celFiles) %in% as.character(remove$V1)]
but none of the 8th entries in "remove" data frame have been removed.
Please advise,
Ana
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.
> And if it's a good idea, then how much to trim.
>
>
> On Sat, Oct 10, 2020 at 5:47 AM Ana Marija
> wrote:
> >
> > Hi Bert,
> >
> > Another confrontational response from you...
> >
> > You might have noticed that I use the word "outl
interpret the plot. I was hoping someone here knows
that and can help me.
Ana
On Fri, Oct 9, 2020 at 11:31 AM Bert Gunter wrote:
>
> I recommend that you consult with a local statistical expert. Much of what
> you say (outliers?!?) seems to make little sense, and your statistical
> k
sd
FQC.10090295 0.0327 0.002678 0.0517
FQC.10119363 0.0220 0.000978 0.0313
FQC.10132112 0.0275 0.002088 0.0457
FQC.10201128 0.0169 0.000289 0.0170
FQC.10208432 0.0443 0.004081 0.0639
FQC.10218466 0.0116 0.000131 0.0115
...
the distribution is not normal, it is right-skewed.
Cheers,
Ana
On Fr
NP[SNP$density>400,]
and plot it again:
p <- ggplot(a, mapping = aes(x = mean, y = var))
p <- p + geom_density_2d() + geom_point() + my.theme + ggtitle("SNPS_red")
On Thu, Oct 8, 2020 at 3:52 PM Ana Marija wrote:
>
> Hello,
>
> I have a data frame like this:
>
>
e ellipses-contours?
2. how do I extract from my data frame the points which are outside of ellipses?
Thanks
Ana
snps.pdf
Description: Adobe PDF document
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4:ncol(mt)) mt[,i] <- 1 + (names(mt)[i]== mt$PLATE)
Thanks!
On Tue, Sep 29, 2020 at 12:08 PM Ana Marija wrote:
>
> HI Bert,
>
> thank you for getting back to me.
> I tried this:
>
> > dat <- cbind(mc, matrix(0,ncol = 34))
> > head(dat)
> FID IID PLATE 1
NA NA NA NA NA NA NA
...
so this gives me the correct columns. Now is the question of how to
replace NA with 2 id column name matches the rownname in PLATE column
with 2 otherwise it is 1.
Cheers,
Ana
On Tue, Sep 29, 2020 at 11:46 AM Bert Gunter wrote:
>
>
se value.var to override.
Please advise,
Ana
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and provide commented, m
osition 1 taken as TRUE when
assigning to type 'logical' (column 6 named 'PHENO')
Please advise,
Ana
On Wed, Sep 23, 2020 at 2:48 PM Jeremie Juste wrote:
>
>
> Hello Ana Marija,
>
> I cannot reproduce your error,
>
> with a$PHENO=ifelse(a$PLASER==2 |a$RTNPTHY==2, 2, ifelse(
, 2020 at 11:43 AM Ana Marija wrote:
>
> Hello,
>
> I have a data frame as shown bellow.
> I want to create a new column PHENO which will be defined as follows:
> if CURRELIG==1 -> PHENO==1
> in the above subset those that have:
> PLASER==2 -> PHENO==2
> and
>
1 1 2
fam5709 G57091 1 1
fam5713 G57131 1 1
fam5715 G57151 1 1
fam5718 G57181 1 1
Please advise,
Ana
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HI Jim,
fantastic solution!
Thank you so much!!!
Ana
On Thu, Sep 17, 2020 at 6:01 PM Jim Lemon wrote:
>
> Hi Ana,
> Sorry it's not in ggplot, but it may help:
>
> d<-read.table(text="CHR counts name
> 1 193554 old
> 2 220816 old
> 3 174350 old
> 4
show counts per CHR in "old" and "new" side by side.
Please advise,
Ana
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% had Type 1. (my TD covariate is reference for
the type of diabetes) In the attach is the description of the data.
Cheers,
Ana
On Tue, Sep 15, 2020 at 7:59 PM David Winsemius wrote:
>
>
> On 9/15/20 8:57 AM, Ana Marija wrote:
> > Hi Abby and David,
> >
> > Th
ect or what
kind of conclusion I can draw from that?
Thanks for all your help
Ana
On Tue, Sep 15, 2020 at 1:26 AM David Winsemius wrote:
>
> There is a user-group for PLINK, easily found by looking at the page you
> cited. This is not the correct place to submit such questions.
>
>
sorry not replace with NA but with empty string for a name, for example
for example this:
> geneSymbol["Ku8QhfS0n_hIOABXuE"]
Ku8QhfS0n_hIOABXuE
"MACC1"
would go when I subject it to
> geneSymbol["Ku8QhfS0n_hIOABXuE"]
Ku8QhfS0n_hIOABXuE
On Mon,
better way to do this from the data I already have?
Thanks
Ana
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ed for tutorials also. This list cannot
> substitute for such homework on your own.
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County&qu
It seems that "treatment" and "patient" are just vectors.
> treatment
[1] "treat" "treat" "treat" "treat" "treat" "control" "control"
[8] "control" "control" "cont
uot;treatment"
> str(treatment)
chr [1:10] "treat" "treat" "treat" "treat" "treat" "control" "control" ...
but this is not the format I need.
On Fri, Jul 31, 2020 at 9:18 PM Ana Marija wrote:
>
> Hello,
>
>
Hello,
I have this file:
> a=load("paired_example.Rdata")
> a
[1] "rawdata" "treatment" "patient"
I can extract "rawdata" with:
dat<-local(get(load("paired_example.Rdata")))
Can you please advise how
aparecen en la pestaña de
Análisis y empezar a aplicar algunos análisis.
Yo sé que tal vez se dediquen sólo a trabajar con R (pero yo recién descubro
esta interfase del RCmdr y me resulta más amigable, soy psicóloga y hago
psicometría)
Desde ya, muchísimas muchas gracias desde Argentina!
Dra. Ana
dediquen sólo a trabajar con R (pero yo recién descubro
esta interfase del RCmdr y me resulta más amigable, soy psicóloga y hago
psicometría)
Desde ya, muchísimas gracias desde Argentina!
Dra. Ana Kohan Cortada CIIPME-CONICET
155 0441827
El viernes, 10 de julio de 2020 07:25:50
Thank you so much as.character(r) indeed resolved the issue!
On Sat, Jun 20, 2020 at 3:47 AM Ivan Krylov wrote:
>
> On Fri, 19 Jun 2020 19:36:41 -0500
> Ana Marija wrote:
>
> > Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1),
> > "\n"),
but I try to avoid extras
>
> make your for statements:
>
> for ( a in rownames(f1) ) {
>
> # a will now be a row number rather than the value, so replace ' a ' in
> the paste0 with: f1[ a, 1]
>
> so
>
> ext <- paste0( "/ld/human/pairwise/",
>
SNPs at the time and I need to do that for 300 pairs
On Fri, Jun 19, 2020 at 6:42 PM Rasmus Liland wrote:
>
> On 2020-06-19 14:34 -0500, Ana Marija wrote:
> >
> > I have two files (each has 300 lines)like this:
>
> The example looks quite similar to the R example in
&g
u may have something that adds it but better to use
> something that works. So try using:
>
> library(readr)
> f1 <- read_tsv("1g.txt", col.names=F)
>
> This will give you a tibble with f1$X1 with the file in it
>
> then loop it with (a in as.list(f1[,1])
>
> Ot
en compressed file '1000GENOMES:phase_3:KHV.rds', probable
reason 'No such file or directory'
> lapply(r[1:4], function(x) {
+ jsonlite::fromJSON(jsonlite::toJSON(httr::content(x)))
+ })
Error in lapply(r[1:4], function(x) { : object 'r' not found
Am I am doing here some
>
> r <- GET(paste(server, ext, sep = ""),
> content_type("application/json"))
>
> # You presumably need to do something with 'r' at the
> moment its over written by the next loop.. were
> # you appending
and output every line of result in list.txt
The process is illustrated in the attachment.
Please help,
Ana
lists.pdf
Description: Adobe PDF document
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proximate in the presence of ties
as I understand high p-values here say I cannot claim statistical
support for a difference, but low p-values are not evidence of
sameness?
D should be the maximum difference between the two probability distributions?
On Wed, Jun 17, 2020 at 3:06 PM Ana Marija wrote:
>
&g
99937, num df = 1454159, denom df = 1454159, p-value = 0.7057
alternative hypothesis: true ratio of variances is not equal to 1
95 percent confidence interval:
0.9970808 1.0016750
sample estimates:
ratio of variances
0.9993739
Or some other test makes more sense?
Thanks
Ana
qq-plots-c
np="MARKER",suggestiveline
= F, genomewideline = F,main = "Gokind old",col = c("red2", "orange",
"gold1","springgreen4", "dodgerblue",
"darkorchid1","orchid1"),ylim=c(0,9),cex = 0.6)
in this qqman function.
C
og,chr="CHR",bp="POS",p="META_pval",snp="MARKER",ylim
= c(0, 10))
dev.off()
Thanks
Ana
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PLEASE do rea
HI Jim
thank you so much! This is amazing answer!!!
Ana
On Sat, Jun 13, 2020 at 4:09 AM Jim Lemon wrote:
>
> Right, back from shopping. Since you have fourteen rows containing NAs
> and you only want seven, we can infer that half of them must go. As
> they are neatly divided int
opriate logic to get rid of only the
> ones you don't want.
>
> Jim
>
> On Sat, Jun 13, 2020 at 12:50 PM Ana Marija
> wrote:
> >
> > Hi Rasmus,
> >
> > thank you for getting back to be, the command your provided seems to
> > add all 11 NAs to 2s
> &
; > > On Sat, Jun 13, 2020 at 10:46 AM Ana Marija wrote:
> > > >
> > > > I am trying to make a new column
> > > > "pheno" so that I reduce the number
> > > > of NAs
> > >
> > > it looks like those two NA values in
>
exclude = NULL)
12
859 828 11
Am I am doing something wrong?
Thanks
Ana
On Fri, Jun 12, 2020 at 8:06 PM Jim Lemon wrote:
>
> Hi Ana,
> From your desired result, it looks like those two NA values in PLASER
> are the ones you want to drop.
> If so, try this:
>
> b
,1)
> table(b$pheno, exclude = NULL)
12
859 828 11
I would like to reduce this number of NAs to be 7
so I would like to have in "pheno column"
7 NAs
825 2s (825=691+14+70+7+43)
and the rest would be 1s (866=1698-7-825)
How can I change the above command t
some shown on the x-axis?
On Thu, Jun 11, 2020 at 4:39 PM wrote:
>
> Your dots are too big!
>
> Add
>
> geom_points(... , size = 1
>
> May need to play... 0.5 or 0.1?
>
> On 11 Jun 2020 22:26, Ana Marija wrote:
>
> I tried it,
> ggplot( data = tmp.tidy) +geom
I tried it,
ggplot( data = tmp.tidy) +geom_point( aes(y = BP,x = CHR,color=key)
,position = "jitter" )
I got the attached
On Thu, Jun 11, 2020 at 4:18 PM wrote:
>
> Try adding
> position = "jitter" to the geom_point(...
>
>
>
> On 11 Jun 2020 21:41, Ana M
Hello,
I tried your code and this is what I got
I really need two groups side by side shown per chromosome as it is here:
https://imgur.com/a/pj40c
on the image there are 4 groups I do have only two
On Thu, Jun 11, 2020 at 11:52 AM wrote:
>
> On 2020-06-11 15:59, Ana Marija wrote:
>
me, and CHR would go from 1 to 22
On Thu, Jun 11, 2020 at 9:26 AM wrote:
>
> On 2020-06-11 14:54, Ana Marija wrote:
> > Hello,
> >
> > I expected it to look like this:
> > https://imgur.com/a/pj40c
> >
>
> Ah - so all on the one plot? - so you don't want a
m 0.952 0.475 0.529 0.255 0.295 ...
Unfortunately qqman doesn't do this kind of overlay of two plots
On Wed, Jun 10, 2020 at 11:24 PM John wrote:
>
> On Wed, 10 Jun 2020 15:36:11 -0500
> Ana Marija wrote:
>
> > Hello,
> >
> > I have a data frame like this:
> &g
ssoc.logistic.jpeg")
manhattan(results_log,chr="CHR",bp="BP",p="P",snp="SNP", main =
"Manhattan plot:logistic")
dev.off()
this code does work with another data set, the jpeg() does work. I
will try now with PNG
On Wed, Jun 10, 2020 at 5:17 PM Jim Le
t;SNP", main =
"Manhattan plot: logistic")
dev.off()
but I am getting:
Error in plot.window(...) : need finite 'ylim' values
Calls: manhattan ... do.call -> plot -> plot.default -> localWindow ->
plot.window
Execution halted
Please advise,
Thanks
Ana
_
Hi Rui,
thank you so much, that is exactly what I needed!
Cheers,
Ana
On Wed, Jun 3, 2020 at 11:50 AM Rui Barradas wrote:
>
> Hello,
>
> If you want to filter out rows with any of the values in a 'unwanted'
> vector, try the following.
>
> First, create a test data se
created just remove any row that contains any of those variables.
Thanks
Ana
On Wed, 3 Jun 2020 at 11:00, Bert Gunter wrote:
> I suggest that you forget all that fancy stuff (and this is not a use
> case for regular expressions).
> Use %in% with logical subscripting instead -- basic R func
('^E11', x, value = TRUE))
d1=unlist(s1)
d11=unique(d1)
> d11
[1] "E11" "E119" "E113" "E115" "E111" "E114" "E110" "E118" "E116" "E112"
[11] "E117"
I need help with changing this command
Hi Jim,
not in this case, but thanks for asking!
Ana
On Mon, Jun 1, 2020 at 10:04 PM Jim Lemon wrote:
>
> So recombination sticks out its foot before us. Do you want to account
> for gene linkage?
>
> JIm
>
> On Tue, Jun 2, 2020 at 11:55 AM Ana Marija
> wrote:
>
r","Chr"))
nn2<-merge(nn1,ret1,by=c("Marker","Chr"))
> Marker3<-nn2$Marker
> length(Marker3)
[1] 3742962
> Marker4<-nn1$Marker
> length(Marker4)
[1] 373
On Mon, Jun 1, 2020 at 8:50 PM Ana Marija wrote:
>
> Hi David,
>
> that is a
43494 9
How would I rewrite this code so that is merging by Chr and Marker
column? It seems that a Marker can be under a few Chr.
On Mon, Jun 1, 2020 at 8:41 PM David Winsemius wrote:
>
>
> On 6/1/20 5:40 PM, Ana Marija wrote:
> > Hi Jim,
> >
> > thank you so m
.
Cheers
Ana
On Mon, Jun 1, 2020 at 7:31 PM Jim Lemon wrote:
> Hi Ana,
> Not too hard, but your example has all the "marker" fields in common.
> So using a sample that will show the expected result:
>
> neu1<-read.table(text="Chr BP Marker MAF A1 A2 Directio
:A 0.0982587 A G - 0.272936
1608
2234642 1 14726 1:14726:G:A 0.1340170 A G - 0.594538
1608
Is there is a way to create another 3 data frames, say neu2, nep2, ret2
which would only contain lines that have the same entries in Marker column
for all 3 data frames?
Thanks
Ana
0.4156 G A + 0.484813 1641
2 10 10645 10:10645:A:C 0.216027 C A + 0.73597 1641
Can you please tell me what colClasses=colClassvec suppose to do?
Thanks
Ana
On Mon, Jun 1, 2020 at 4:13 PM David Winsemius
wrote:
>
> On 6/1/20 1:37 PM, Ana Marija wrote:
&g
ple keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
>
> On Mon, Jun 1, 2020 at 1:38 PM Ana Marija
> wrote:
>
>> Hello,
>>
>> I have a dataframe like this:
>>
>> Chr
ble("gokind.neuropathy.fin", header=T,stringsAsFactors=FALSE)
and every column is numeric. How to say have all numeric ones stay numeric
like: Chr, BP, MAF, pValue, N
Thanks
Ana
[[alternative HTML version deleted]]
__
R-help@r-projec
ous(breaks
= unique(d))
ed
where:
> head(e)
ESRD pheno
11 1
21 1
31 2
41 1
51 1
> sapply(e,class)
ESRD pheno
"integer" "factor"
On Fri, May 22, 2020 at 1:52 PM Ana Marija wrote:
>
> Hello,
>
> I made t
Hello,
I made the plot in attach via:
ed<-ggplot(e) +
geom_bar(aes(x = ESRD, fill =
factor(pheno,labels=c("control","case"+scale_fill_manual(values=c("#56B4E9","#E7B800"))+labs(fill="pheno")
())
I am getting the plot in attach, while my results should be more in
this range like on the plot here:
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/variable.cgi?study_id=phs18.v2.p1=19980=154=2864=62=1==1
On Fri, May 22, 2020 at 12:18 AM Eric Berger wrote:
>
>
ou the whole dataset if you would like to try with it
On Thu, May 21, 2020 at 11:14 PM Jim Lemon wrote:
>
> Hi Ana,
> Just noticed a typo from a hasty cut-paste. Two lines should read:
>
> casehist<-table(cut(aafd$HBAIC[aafd$pheno=="case"],breaks=0:15))
> cont
the result would basically look something like this on in attach or
the overlay of those two plots
On Thu, May 21, 2020 at 5:23 PM Ana Marija wrote:
>
> Hello,
>
> I have a data frame like this:
> > head(a)
> FID IID FLASER PLASER DIABDUR HBA1C ESRD pheno
dth=.5,
position="dodge")
there is 848 who have "case" in pheno column and 892 who have
"control" in pheno column.
I would like to have on y-axis shown percentage of individuals which
have either "case" or "control" in pheno instead of count.
Please advis
5,annotatePval = 0.0001)
but I am getting this error:
Error in textxy(topSNPs$pos, -log10(topSNPs$P), offset = 0.625, labs =
topSNPs$SNP, :
formal argument "cex" matched by multiple actual arguments
Do you by any chance know how to do this?
Cheers
Ana
On Wed, May 20, 2020 at 4:1
Hi Michael,
can you please send me code how that would be done?
Thanks
Ana
On Tue, May 19, 2020 at 11:18 AM Michael Dewey wrote:
>
> Dear Ana
>
> Perhaps paste together SNP and GENE using paste() and then supply that
> as the snp parameter.
>
> Michael
>
> On 19/05/2
SNP=="rs4081570",]
SNPP CHR BP GENE
1 rs4081570 6.564447e-05 19 15918647 UCA1
> a[a$SNP=="rs11867934",]
SNPP CHR BP GENE
1021 rs11867934 6.738066e-06 17 16933404 FLCN
Right now my plot only has SNP name for those 2
Hi Rui,
thank you so much that is exactly what I needed!
Cheers,
Ana
On Fri, May 15, 2020 at 5:12 PM Rui Barradas wrote:
>
> Hello,
>
> I have tried several options and with large dataframes this one was the
> fastest (in my tests, of the ones I have tried).
>
>
> s1 &
ith E10.
Thanks
Ana
On Fri, May 15, 2020 at 12:13 PM Jeff Newmiller
wrote:
>
> Read about regular expressions... they are extremely useful.
>
> df1 <- tot %>% filter_all(any_vars(grepl( '^E10', .)))
>
> It is bad form not to put spaces around the <- assignment.
>
&
s that start with E10...
it would look something like this:
[1] "E102" "E109" "E108" "E103" "E104" "E105" "E101" "E106" "E107"
Thanks
Ana
__
R-help@r-project.o
uot;Populations in millions (log scale)")+
+ylab("Total number of murders (log scale)")+
+ggtitle("US Gun Murders in US 2010")+
+scale_color_discrete(name="Region")+
+theme_economist()
Is this an issue with my d
>
> t.test(x, mu = beta0)$statistic
>
>
> But in this case the estimator is the estimator for the mean value.
>
> Hope this helps,
>
> Rui Barradas
>
> Às 15:54 de 06/05/20, Ana Marija escreveu:
> > Thanks Patrick, so in conclusion this is fine?
> > z-sco
Thanks Patrick, so in conclusion this is fine?
z-score=Beta/StdErr
On Wed, May 6, 2020 at 9:52 AM Patrick (Malone Quantitative)
wrote:
>
> Guessing for Ana, but no, that's a different meaning. Beta/StdErr is a
> z statistic--a test statistic against (usually) the tails of the unit
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