I'd like to use ChIPpeakAnno to do downstream analysis after peak calling by macs2.
But I got some error for toGRanges to upload my results from macs2.
macs <- system.file("/Users/macs2", "/Users/macs2/cz3Rip_vs_cz1Inp_peaks.xls", package="ChIPpeakAnno")
macsOutput <- toGRanges(macs, format="MACS")
Error in read.table(data, header = header, ..., nrows = 5) : no lines available in input In addition: Warning message: In file(file, "rt") : file("") only supports open = "w+" and open = "w+b": using the former
I also tried broadPeak, but still got the error.
Thanks so much~~~