With R, loop over two files at a time - r

Question

Hello my favourite coding experts,
I am trying to loop through two files at a time in R: i.e. take one 'case' file and another 'control' file, create a graph and dump it into a pdf, then take another set of 2 files and do the same and so on. I have a list indicating which file is a case and which is a control, like this:
case control
A01 G01
A02 G02
A06 G03
and so on… which can be reproduced like this:
mylist<- data.frame(rbind(c("A01","G01"),c("A02","G02"),c("A06","G03")))
colnames(mylist)<- c('control', 'case')
I cannot find a way to specify which 2 files to loop through each time.
The file (each file with many variables) are: "/Users/francy/Desktop/cc_files_A01", ""/Users/francy/Desktop/cc_files_A02", "/Users/francy/Desktop/cc_files_A06", "/Users/francy/Desktop/cc_files_G01", "/Users/francy/Desktop/cc_files_G02", "/Users/francy/Desktop/cc_files_G03"
For each set of case and control, I would like to do this:
case<- read.table(file="/Users/francy/Desktop/case_files_A01.txt", sep = '\t', header = F)
case <- case[,c(1,2,19,20)]
colnames(case)<- c("ID", "fname", "lname", "Position")
control<- read.table(file="/Users/francy/Desktop/case_files_G01.txt", sep = '\t', header = F)
control <- control[,c(1,2,19,20)]
colnames(control)<- c("ID", "fname", "lname", "Position")
#t-test Position:
test<- t.test(case[20],control[20])
p.value= round(test$p.value, digits=3)
mean_case= round(mean(case[20], na.rm=T), digits=2)
mean_control= round(mean(control[20], na.rm=T), digits=2)
boxplot(c(case[20], control[20]), names=c(paste("case", "mean", mean_case, sep=":"),paste("control", "mean", mean_control, sep=":")))
And want to create a pdf file with all the boxplots.
This is what I have for now:
myFiles <- list.files(path= "/mypath/", pattern=".txt")
pdf('/home/graph.pdf')
for (x in myFiles) {
control <- read.table(file = myFiles[x], sep = '\t', header = F)
## How do I specify that is the other file here, and which file it is?
case <- read.table(file = myFiles[x], sep = '\t', header = F)
}
Any help is very appreciated. Thank you!

Answer 1

Why not just pass the pairs of files to the loops via a list?
files <- list(
c("fileA","fileB"),
c("fileC","fileD")
)
for( f in files ) {
cat("~~~~~~~~\n")
cat("f[1] is",f[1],"~ f[2] is",f[2],"\n")
}
The first time the loop runs, f contains the 1st element of the list files. Since the first element is a character vector of length two, f[1] contains the first file name of the pair, and f[2] contains the second. See the printed output of the above code, which should hopefully make it clear.

Answer 2

What probably makes more sense in this case, is building up the two filenames from your "list" (a data.frame?) of cases and controls.
If this "list" is present in a data.frame lcc, you could do something like:
for(i in seq(nrow(lcc)))
{
currentcase<-lcc$case[i]
currentcontrol<-lcc$control[i]
currentcasefilename<-paste("someprefix_", currentcase, "_somepostfix.txt")
currentcontrolfilename<-paste("someprefix_", currentcontrol, "_somepostfix.txt")
#now open and process both files...
}

Answer 3

Assuming your list of cases and controls is in an R object (dataframe or matrix) called mylist:
for (x in seq_along(nrow(mylist)) {
case <- read.table(file = paste("/my/path/", mylist[x, "case"], ".txt", sep = ""),
sep = "\t", header = F)
control <- read.table(file = paste("/my/path/", mylist[x, "control"], ".txt", sep = ""),
sep = "\t", header = F)
## your code here ##
}