t))
> >
> > # Loop over your input
> > for (i in 1:nrow(mat)) {
> > # Sort the elements of a row by size.
> > x <- sort(mat[i,])
> > # Increment the corresponding element of the frequency matrix
> > freq[x[1], x[2]] <- freq[x[1], x[2]] + 1
> &g
x.
>
>
> B.
>
>
>
> On Oct 6, 2015, at 4:59 PM, Hermann Norpois <hnorp...@gmail.com> wrote:
>
> > Hello,
> >
> > I have a matrix mat (see dput(mat))
> >
> >> mat
> > [,1] [,2]
> > [1,]56
> > [2,]65
Hello,
why do I get NA for the following:
cut (x, seq (0, max(x), by=1), label=FALSE)
[1] 1322 1175 1155 1149 1295 1173 1289 1197 NA 1129
dput (x)
c(1321.55376901374, 1174.35657200935, 1154.02042504008, 1148.60981925942,
1294.6166388941, 1172.45806806869, 1288.31933914639, 1196.26080041462,
Hello,
I have a matrix mat (see dput(mat))
> mat
[,1] [,2]
[1,]56
[2,]65
[3,]54
[4,]55
I want the frequencies of the pairs in a new matrix, whereas the
combination 5 and 6 is the same as 6 and 5 (see the first two rows of mat).
In other words:
Thanks this was very helpful.
@Olivier Crouzet: Yes, round (x) would do the job but it was a principal
confusion ...
2015-10-06 21:57 GMT+02:00 Marc Schwartz <marc_schwa...@me.com>:
>
> > On Oct 6, 2015, at 2:20 PM, Hermann Norpois <hnorp...@gmail.com> wrote:
> >
>
Hello,
I am looking for a possibility to define something like ylim for lines. I
thought, there might be a possibility to define the range of lines by means
of par ("usr") but I did not find the correct syntax. In my toy example I
would like to stop the red line at y=0.3.
Thanks Hermann
toy
Hello,
for a multiple figures plot I am looking for the syntax to put text in the
top left of the margin (of the plot). I want my testfunction plot.figure to
place mtext in the top left of the red margin (created by box("figure",
col="red")).
Can anybody help?
Thanks
Hermann
plot.figure <-
wdunlap tibco.com
On Tue, Apr 14, 2015 at 2:34 PM, Hermann Norpois hnorp...@gmail.com
wrote:
Hello,
I try to open a text file test.txt with the content
* a b d
* z u i h hh
* h bh kk
so that I get a list with each line as a vector with the letters as
elements of the the vector.
My
Hello,
I try to open a text file test.txt with the content
* a b d
* z u i h hh
* h bh kk
so that I get a list with each line as a vector with the letters as
elements of the the vector.
My approach ...
test - scan (test.txt, what=character, sep=\n)
Read 3 items
test.list - lapply (test,
Hello,
My main question is wheter my data is distributed normally. As the
shapiro.test doesnt work for large
data sets I prefer the ks.test.
But I have some problems to understand the completely different p-values:
ks.test (test, pnorm, mean (test), sd (test))
One-sample
Hello,
I have some problems with as.Date.
strDates - c (01/05/1965, 08/16/1975)
dates - as.Date (strDates, %m/%d%/%Y)
dates
[1] NA NA # I expected my dates. What was going wrong?
Thanks
Hermann
[[alternative HTML version deleted]]
__
Hello,
I want to detect Ab not Abc. For a normal vector
test
[1] A Ab GG GA H Abc Gz HU
grep (^Ab$, test)
[1] 2
works well.
For
test.list
[[1]]
[1] A Ab GG GA
[[2]]
[1] H Abc Gz HU
grep (^Ab$, test.list)
integer(0)
doest not work.
Why?
How do I detect exclusively Ab in a list
Hello,
I am looking for a method to eliminate rows dupblicates in a backwards
manner, for instance:
I want to keep A B but not B A (see my data.frame test).
Thanks
Hermann
test
a u
1 A B
2 A C
3 B A
4 B F
5 C A
6 D W
dput (test)
structure(list(a = structure(c(1L, 1L, 2L, 2L, 3L, 4L), .Label
Hello,
having a list like testlist I would like to transform it in dataframe. How
does it work?
Thanks
Hermann
testlist
[[1]]
BP_A SNP_A BP_B SNP_B R2
2 27001689 rs4822747 27002392 rs4820690 0.695642
3 27001689 rs4822747 27004298 rs5761627 0.695642
4 27001689 rs4822747
, Hermann Norpois
hnorp...@gmail.com wrote:
Hello,
having a list like testlist I would like to transform it in dataframe. How
does it work?
Thanks
Hermann
testlist
[[1]]
BP_A SNP_A BP_B SNP_B R2
2 27001689 rs4822747 27002392 rs4820690 0.695642
3 27001689
]]) is nonempty? Your
example isn't -- you did not specify what the return should be on your
list.
Note also that your example test is wrong: the length of the
intersection must =0 not the intersection.
-- Bert
On Sat, Nov 9, 2013 at 12:45 PM, Hermann Norpois hnorp...@gmail.com
wrote
huz[[i]] - sort (chain3)
next
}
}
}
huz - unique (huz)
return (huz)
}
2013/11/9 Hermann Norpois hnorp...@gmail.com
Hello,
I have a list called ja and I wish
Hello,
I have a list called ja and I wish to unify list objects if there is some
overlap.
For instance something like
if (length (intersect (ja[[1]], ja[[2]]) !=0) { union (ja[[1]], ja[[2]] }
but of course it should work cumulatively (for larger data sets).
Could you please give me a hint.
Hello,
having a data frame like test with pairs of characters I would like to
create chains. For instance from the pairs A/B and B/I you get the vector A
B I. It is like jumping from one pair to the next related pair. So for my
example test you should get:
A B F G H I
C F I K
D L M N O P
test
You might try to import your data in GenABEL,
use
as.numeric (gtdata (data))
to get a matrix that delivers you 0,1 or 2 for each snp and id (observation)
and then try prcomp.
Also check this
http://gettinggeneticsdone.blogspot.de/2011/10/new-dimension-to-principal-components_27.html
Thanks. This was helpful.
Hermann
2013/10/17 Bretschneider (R) brets...@xs4all.nl
On 17 Oct 2013, at 13:44 , Hermann Norpois wrote:
Hello,
my dots of 0 and 2 are quite close to the marging. So I would like to move
the 0 and the 2 both towards the 1. I wish to be my dots more centered
Hello,
my dots of 0 and 2 are quite close to the marging. So I would like to move
the 0 and the 2 both towards the 1. I wish to be my dots more centered.
And: I dont need so much space between 0,1 and 2.
How does it work?
I tried:
plot (data, axes=FALSE, main=i, ylab= expression (z^2))
)), z))
but if Genotype is best represented as a factor, that may not be the
most informative type of plot.
Sarah
On Tue, Oct 15, 2013 at 10:23 AM, Hermann Norpois hnorp...@gmail.com
wrote:
Hello,
I would like to plot some values referring to the genotype (which is 0,1
and 2). My
Hello,
I would like to plot some values referring to the genotype (which is 0,1
and 2). My data is organised like this:
head (df)
Genotype z
10 0.07029379
20 2.15739115
30 0.51395897
40 0.48733029
50 0.15584074
60 0.27755294
I tried:
Hello,
I did a pca with over 20 snps for 340 observations (ids). If I plot the
eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot
(rotation[,2]) I see a strange column in my data (see attachment). I
suggest it is an artefact (but of what?).
Suggestion:
I used prcomp this way:
is having extreme values on component 2-4 and then go back and see
if there is something peculiar about their SNPs in the strange region.
Of course, you might have stumbled upon a bug in R, but I doubt so.
Happy hunting!
-pd
On Oct 3, 2013, at 11:41 , Hermann Norpois wrote:
Hello,
I
Hello,
I have a question concerning the output of leveneTest. I don't understand
the 7 in my output
Levene's Test for Homogeneity of Variance (center = median)
Df F value Pr(F)
group 2 0.0173 0.9829
7# Where does this number come from?
Thanks.
Hermann
res
group.ID
Hello,
i attached an example with two plotted vectors, respectively. And you might
see that the y and x axis are not the same scale (e.g. the third and the
last plot).
I would prefer them to be the same scale.
A toy example:
a - c (1,2,3,4,5,6,9,20)
b - c (0.2,0.4,0.6,1,0.5,1,1,0.1)
plot
Hello,
I tried to compute the covariance (between the columns) of a matrix with
20.
This failed ...
Error: cannot allocate vector of size 691.2 GB
Ok, this is rather huge. But ... On the other hand ... Is there an
alternative to cov?
Maybe one could combine combn with cov - so it is rather
Hello,
I would like to do a pca with princomp.
I have a dataset with different observations for each row and for different
variables for each column (test.z). If I understood it correctly this is
the way the data should be structured for princomp. But it does not work.
But if I transpose the
think what you want is
?try ##or
?tryCatch
## The second is more flexible but slightly more complicated.
to trap the error and perhaps refit the model without interaction?
Cheers,
Bert
On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois hnorp...@gmail.com
wrote:
Hello,
I use glm
Hello,
I use glm within a function testing for the appearence of the coexistence
of (minor allels in a subset of) snps. And then I extract the
Pr(|z|)-value for the interaction. Principally it works but sometimes the
function stops because this value for the interaction is NA. For
instance,
Hello,
how can I retrieve electively data from a summary file, for instance I
would like to get the Pr of Coefficients
Thanks
summary (plasma_glm_1)
Call:
glm(formula = ESR ~ fibrinogen, family = binomial(), data = plasma)
Deviance Residuals:
Min 1Q Median 3Q Max
-0.9298
Hello,
I have a matrix m and I want to know how often does 1 (or !0) simultanously
appear in A and REF, B and REF, C and REF.
So actually I wish to automate following expression:
length (which (m[,1]!=0m[,4]!=0))
[1] 2
length (which (m[,2]!=0m[,4]!=0))
[1] 1
Thanks
Hermann
m
A B C REF
Hello,
I have a nice function that makes an image of an matrix
e.g.:
qt[1:3,1:3]
rs655246 rs943795 rs955612
rs655246 NA NA NA
rs943795 9.610070e-04 NA NA
rs955612 5.555616e-05 7.915982e-07 NA
myimage - function(x, cex.axis = 0.7,
of class dtCMatrix
#rs1 rs2 rs3
#rs1 . . .
#rs2 1 . .
#rs3 2 1 .
A.K.
- Original Message -
From: Hermann Norpois hnorp...@gmail.com
To: r-help r-help@r-project.org
Cc:
Sent: Wednesday, May 15, 2013 3:57 PM
Subject: [R] matrix - pairwise comparison
Hello,
I fail to tranfer data from a dataframe to a matrix.
jam is from a dataframe (and belongs still to the class dataframe) and
should look like m (see below).
jam
vec1 vec3 d1 d2
1 172 173 223 356
dput (jam)
structure(list(vec1 = 172L, vec3 = 173L, d1 = 223L, d2 = 356L), .Names =
Hello,
I would like to do something with a matrix:
1) The columns should be compared pairwise.
2) And the result should be a matrix.
I try to illustrate the problem with a testset.
m
rs1 rs2 rs3
[1,] 1 1 1
[2,] 0 1 0
[3,] 2 0 1
dput (m)
structure(c(1, 0, 2, 1, 1, 0, 1,
Hello,
I would like to transform a character vector into a binary vector
(keine and become 0 and the rest 1).
dput (scm)
c(keine, , keine, Erstgradverw., Mutter, Erstgradverw.,
Erstgradverw., keine, , Vater, Erstgradverw., keine,
keine, keine, keine, , Erstgradverw., keine, keine,
Hello,
I open some files in a directory and get a list.
open.list - sapply (namen, function (x) {file - list.files (ddir,
pattern=x, full.names=TRUE) # namen is vector and each element detects a
special file to open
file - read.table (file)
Hello,
I wish to count how often zero (0) appears in the vector test.
test
[1] 1 1 1 1 1 1 2 1 1 1 0 2 0 1 1 0 0 0 1 1 1 0 1 2 1 1 1 1 1 1
I think of something like ...
sapply (test, function (x) if (x==0 ...
... but actually I dont know how to carry on.
Could anybody give me a hint?
Very simple. And great.
Thanks.
2013/1/3 Sarah Goslee sarah.gos...@gmail.com
sum(test == 0)
On Thu, Jan 3, 2013 at 5:49 PM, Hermann Norpois hnorp...@googlemail.com
wrote:
Hello,
I wish to count how often zero (0) appears in the vector test.
test
[1] 1 1 1 1 1 1 2 1 1 1 0 2 0 1 1
Hello,
I have start and end coordinates from different experiments (DNase
hypersensitivity data) and now I would like to combine overlapping
intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101
are combined to 30-101. But 49-101 and 70-103 would not be combined because
they
Hello,
my data is sorted by start.ens (see below). And now I would like to extract
all rows (so called* defined row*s) with type==Expression - subset (df,
type==Expression) - and the aforegoing type==DNase HS (which is not
necessarly row n-1 - assumung that the defined row is n). I dont know how
Hello,
I have a vector (numeric) v- c(a,b,c,d,e) and I want to create the vector
n-c(b-a,c-b,d-c,e-d). How can I do that?
Thank you
Hermann
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, 7L)), .Names = c(chrom, start, end, peak
), row.names = c(NA, -6L), class = data.frame)
Thanks for some instructions.
Hermann Norpois
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Hello,
I have a list with gene names, fold changes (=expression level) and
chromosomes.
Names fold change chromosome
hz 1.5 2
If I plot fold change versus chromosome (or vice versa):
plot (ch, fc)
I see only the chromosomes with numbers but not those with letter (x
. It was not detected by
(.packages(all.available=TRUE))
if installed in the R library.
Thanks
Hermann Norpois
This was my try to install the lumi package:
source (http://bioconductur.org/biocLite.R;)
Fehler in file(filenaReme, r, encoding = encoding) :
kann Verbindung nicht öffnen
Zusätzlich
and on but not on fc or attr(mydata, 'fc').
Is there a possibility to use function and having access to attr AND
newdata?
Thanks
Sincerely
Hermann Norpois
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