readPeakFile reads in peak coordinates from MACS xls files as zero-based although they are 1-based

[frankRuehle]

Hello, when reading in MACS2/3 xls files with readPeakFile(), the peak coordinates are treated as zero-based like bed files. I.e. readPeakFile adds 1 to all start coordinates. However, the coordinates in those xls files are 1-based and should not be interpreted as zero-based.

peaks.xls readPeakFile("peaks.xls")

R version 4.1.2 ChIPseeker 1.30.0

[GuangchuangYu]

https://macs3-project.github.io/MACS/docs/callpeak.html:

Coordinates in XLS is 1-based which is different from BED format. When --broad is enabled for broad peak calling, the pileup, p-value, q-value, and fold change in the XLS file will be the mean value across the entire peak region, since peak summit won’t be called in broad peak calling mode.

please use bed file instead.