Error with reduce in CallPeaks function if no peaks are called

[zrcjessica]

I am using CallPeaks to call cell type-specific peaks and have both group.by and idents arguments set. E.g.:

DefaultAssay(dat) <- "peaks"
peaks <- CallPeaks(
    object = dat,
    group.by = "predicted.id",
    idents = celltype,
    macs2.path = "/iblm/netapp/home/jezhou/anaconda3/envs/r4/bin/macs2",
    outdir = file.path("test", celltype),
    name = celltype,
    additional.args = "--nomodel --shift 100 --extsize 200 --qval 5e-2 -B --SPMR",
    cleanup = FALSE)

In my example, no peaks were found for the cell type I was testing. Because the default value for combine.peaks is TRUE, the function still attempted to call reduce on the GRanges object that results from the peak calling. This leads to an error message:

No peaks found for Cck+
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘reduce’ for signature ‘"NULL"’
Calls: CallPeaks -> CallPeaks.Seurat -> reduce -> <Anonymous>
Execution halted

This could be fixed by setting combine.peaks to FALSE; however, I wonder if it would be helpful for the function to automatically recognize when the GRanges object is empty and handle the error instead of crashing the job.

Thanks!

[timoast]

Thanks for reporting, it would make sense to do a check on the number of peaks returned for each cell type before trying to combine them to avoid this error. We'll try to add this in a future release