Question

So I’ve created an object of 12 binary files. As part of the analysis that I want to do, I compare one of the 12 against the other 11, using functions to do some analysis.

i.e.

In loop one, object$1 compared against object$1 2:12,

loop two, object$2 against object$ 1,3:12

…

loop 12, object$12 against object$1[1:11]

I can do it on a small scale manually, by specifying the file names. But as it involves comparing all 12 against each other, and I have many groups of 12 files (250 files in total) to work ok, how I automate this?

The eventual output is a data frame, so I’d like that to be created in each loop too (with the relevant file name, like object$1.csv or something).

firstbatch <-bams[1:12] #bams is character vector of the files
bedfile <- "filename.bed"
my.counts <- getBamCounts(bed.file = bedfile, bam.files = firstbatch) #creates object
my.test <- firstbatch$1
my.ref.samples <- firstbatch$2...firstbatch$12
series of functions comparing $1 against 2:12

Answer 1

maybe you cold use this procedure :

a <- combn(12,2)   # will give you all possible combinations 

for (i in 1:dim(a)[2]) {      #loops over all possible combinations

firstbatch[ a [1,i]]    # first sample name to compare
firstbatch[ a [2,i]]    # second sample name to compare against
...
}