Displaying 10 results from an estimated 10 matches for "chr22".
Did you mean:
chr2
2011 Oct 17
2
Histogram for each ID value
I have a dataframe in the general format:
chr1 0.5
chr1 0
chr1 0.75
chr2 0
chr2 0
chr3 1
chr3 1
chr3 0.5
chr7 0.75
chr9 1
chr9 1
chr22 0.5
chr22 0.5
where the first column is the chromosome location and the second column is
some value. What I'd like to do is have a histogram created for each chr
location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and
chr22). I am just having a hard time getting everything to...
2012 Feb 23
1
segfault when using data.table package in conjunction with foreach
...uot;OK\n")
}
ans
}
require(foreach)
require(doMC)
registerDoMC(cores=2)
num <- 8891
nr <- 500000000L #500 million rows at a time
MMM <- foreach(IT = 1:2) %dopar% {
require(data.table)
if (IT==1){ x <- system.time({computeAllPairSums(
paste(GERMLINE,"bc.chr22.q.20.file",sep=''),num,nr)}) } #Run it on
regular file PID 6489, 24 gb
if (IT==2){ z <- system.time({computeAllPairSums.gz(
paste(GERMLINE,"bc.chr22.q.20.gz",sep=''),num,nr)}) } #Run it on gz
file PID 6490, 24 gb
}
MY R OUTPUT/ERROR:
MMM <- foreach(IT = 1...
2017 Jul 12
2
submitting R scripts with command_line_arguments to PBS HPC clusters
...it is run from a regular terminal ..)
Please may I ask, how do you usually submit the R scripts with command line
arguments to PBS HPC schedulers ?
qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \
-v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \
-e script.efile.chr22 \
-o script.ofile.chr22 \
script.R
Thank you very very much !
-- bogdan
[[alternative HTML version deleted]]
2008 Feb 02
2
transforming one column into 2 columns
Hello
I have a data frame and one of its columns is as follows:
Col
chr1:71310034
chr14:23354088
chr15:37759058
chr22:18262638
chrUn:31337214
chr10_random:4369261
chrUn:3545097
I would like to get rid of colon (:) and replace this column
with two new columns containing the terms on each side of the colon. The new columns
should look as follows:
Col_a Col_b
chr1 71310034
chr14 23354088...
2017 Jul 12
0
submitting R scripts with command_line_arguments to PBS HPC clusters
...minal ..)
>
>Please may I ask, how do you usually submit the R scripts with command
>line
>arguments to PBS HPC schedulers ?
>
>qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \
>-v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \
>-e script.efile.chr22 \
>-o script.ofile.chr22 \
>script.R
>
>Thank you very very much !
>
>-- bogdan
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and...
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
...print(CHR)
qsub shell script test.sh:
> #!/bin/bash
>
> #Note: the single quote '...' around the --args ... "..." "..." is important!
> R CMD BATCH --no-save --no-restore '--args TUMOR="tumor.bam" GERMLINE="germline.bam" CHR="chr22"' test.R test.Rout
then you submit with a qsub with all the options you specified the test.sh
qsub .... test.sh
cheers
Peter
> On 12. Jul 2017, at 03:01, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote:
>
> This sounds like an operating system specific question, in...
2012 Jun 21
2
Simple Question?
...chrX 155270560
9 chr8 146364022
10 chr9 141213431
11 chr10 135534747
12 chr11 135006516
13 chr12 133851895
14 chr13 115169878
15 chr14 107349540
16 chr15 102531392
17 chr16 90354753
18 chr17 81195210
19 chr18 78077248
20 chr20 63025520
21 chrY 59373566
22 chr19 59128983
23 chr22 51304566
24 chr21 48129895
I want to drop the "chr" and order the chrom column in ascending order with
X & Y at the end.
I have tried converting the chrom into a character vector and using the
strsplit function, but then I have to circle back and do a lot of editing
to make it w...
2008 Feb 08
1
convertin a data frame column from character to numeric
I have a data.frame with all character columns, I would like to convert the last two columns into numeric.> x[1:5, ] chrN start end 1 chr1 71310034 71310064 2 chr14 23354088 23354118 3 chr14 71310034 71310064 4 chr15 37759058 37759088
5 chr22 18262638 18262668 > apply(x, 2, FUN = mode) chrN start end "character" "character" "character"
____________________________________________________________________________________
Be a better friend, newshound, and
[[alternativ...
2011 Jul 27
2
Writing a summary file in R
Hello,
I have an input file:
http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt
where col 1 is chromosome, column2 is start of region, column 3 is end of
region, column 4 and 5 is base position, column 6 is total reads, column 7
is methylation data, and column 8 is the strand.
I would like a summary output file such as:
2011 Apr 15
1
Whole genome searching of 100bp "D" sequence
...chr6", "chr7", "chr8",
"chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16",
"chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY")
#access/group the by subset of annotation
annotGr <- exons(txdb)
#annotGr <- cds(txdb)
wholeGenomeMatch <- function()
{
for(i in chrList)
{
#matches on plus strand
matches.plus.strand <- matchPattern(query.plus, Hsapiens[[i]],...