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","strand")
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.
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