CallPeaks() function on multiple fragments.tsv.gz files

[hongruhu]

Hi I was wondering if I could use the CallPeaks() function on multiple fragments.tsv.gz files' paths?

For example I have 3 files and they have different fragments, A.tsv.gz, B.tsv.gz, and C.tsv.gz:

        1: chr1  3000137  3000371 TGCTTCGTCCATTGAG-1  1
        2: chr1  3000147  3000361 AGGCGAAAGCAATAAC-1  6
        3: chr1  3000189  3000366 TCAAAGCAGTCGTACT-1 10

        1: chr1  3000206  3000282 AGGCCCAAGTAACATG-1  3
        2: chr1  3000225  3000280 TACTAGGCAATTAGGA-1  1
        3: chr1  3000322  3000587 TTAGCGAAGTCTCGAT-1  2

        1: chr1  3000035  3000294 AATGTCGCATTGCCTC-1  7
        2: chr1  3000086  3000280 CTAGGGCGTACAAGCG-1 20
        3: chr1  3000149  3000190 TCGCAGGCACTGTCAA-1  3

Is there anyway to get the cell x peak matrix for each of the 3 datasets with the same features(peaks)

Thanks!

[timoast]

The CallPeaks() function can use a list of fragment files, or if there are multiple fragment files linked to the object they will all be used. Similarly for FeatureMatrix(), all the fragment files linked to the object are used

[AmosFong1]

@timoast If there are a list of fragment files, can you still use the group.by argument to run MACS2 on subsets of cells?