search for: chr22

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...

...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...

...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]]

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...

...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...

...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...

...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...

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...

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:

...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]],...