I have been doing a three way analysis of ChIP-Seq data (histone modifications) using ChIPpeakAnno and I am having difficulty exporting my data. I am able to find overlapping peaks for my three peak files, but am unable to write out the file using any "write" function that I have tried due to the differing numbers of rows. I get this same error while trying to export my enrichedGO data file as well. I have searched around and am unable to configure a solution so if anyone can help me out, I'd really appreciate it!
I am able to call the correct object from the overlappingPeaks object and can print it out in R, but am unable to export.
>Ol <- findOverlapsOfPeaks(d3.p300.TGR, d3.k4m1.TGR,d3.k27Ac.TGR, maxgap = 1000, minoverlap = 1L, ignore.strand = TRUE, connectedPeaks = "min")
>annotated.overlaplist <- Ol$overlappingPeaks
Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 30641, 251, 117
Many thanks for any assistance.