[R] Loops for repetitive task

[Peter Alspach]

Tena koe

Try something along the following lines:

chrData <- vector('list', 22)
names(chrData) <- paste('chr', 1:22, sep='')

for (i in 1:length(chrData))
{
  chrData[[i]] <- read.table(file=paste('chr', i, '.out.txt', sep=''), header=F)
  ...
}

HTH ....

Peter Alspach

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of a217
> Sent: Wednesday, 10 August 2011 4:32 p.m.
> To: r-help at r-project.org
> Subject: [R] Loops for repetitive task
> 
> Hello,
> 
> I have an R script that I use as a template to perform a task for
> multiple
> files (in this case, multiple chromosomes).
> 
> What I would like to do is to utilize a simple loop to parse through
> each
> chromosome number so that I don't have to type the same code over and
> over
> again in the R console.
> 
> I've tried using:
> 
> for(i in 1:22){
> etc..
> }
> 
> and replacing each chromosome number with [[i]], but that did not seem
> to
> work.
> 
> Below is the script I have. Basically everywhere you see a '2' I would
> like
> there to be an 'i' so that the script can be applied in a general
> sense.
> ################################Code###############################
> 
> chr2.data<-read.table(file="chr2.out.txt", header=F)
> colnames(chr2.data)<-
> c("chr","start","end","base1","base2","totalreads","methylation","stran
> d")
> splc2<-split(chr2.data, paste(chr2.data$chr))
> chr2.df<-as.data.frame(t(sapply(splc2, function(x)
> list(TR=NROW(x[['totalreads']]),    RG1=sum(x[['totalreads']]>=1),
> percent=(NROW(x[['totalreads']]>=1)/sum(x[['totalreads']]))))))
> chr2.df.summ<-as.data.frame(t(sapply(splc2, function(x)
> summary(x$methylation))))
> chr2.summ<-cbind(chr2.df,chr2.df.summ)
> 
> ##################################################################
> 
> 
> Here are some sample input files in case you'd like to test the code:
> ##########
> # chr1.out.txt
> ##########
> chr1	100	159	104	104	1	0.05	+
> chr1	100	159	145	145	1	0.04	+
> chr1	200	260	205	205	1	0.12	+
> chr1	500	750	600	600	1	0.09	+
> 
> ##########
> # chr2.out.txt
> ##########
> chr2	100	200	105	105	1	0.03	+
> chr2	100	200	110	110	1	0.08	+
> chr2	300	400	350	350	0	0	+
> 
> 
> The code works perfectly fine just typing everything out by hand, but
> that
> is very inefficient given that there are 24 chromosomes for each
> dataset. I
> am just looking for any suggestions as to how I can write a general
> version
> of this code.
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/Loops-for-
> repetitive-task-tp3732022p3732022.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at 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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