Error in cursor:(cursor + seq - 1) : result would be too long a vector running plotPeakProf2

[johannesnicolaus]

Hello, I got an error trying to run plotPeakProf2 for my data when I specify the upstream and downstream parameters. When it is not specified, it works ok.

The command:

plotPeakProf2(gr2, TxDb = gr1, type = "body", by = "gene", nbin = 50, upstream = 500, downstream = 500)

I'm not sure how it can be replicated, I can send the input files if needed. I tried running this using different GR objects and nothing worked.

The output

#
#.. 'TxDb' is a self-defined 'GRanges' object...
#
>> binning method is used...2025-01-22 11:06:47 AM
>> preparing body regions by name... 2025-01-22 11:06:47 AM
>> preparing tag matrix by binning...  2025-01-22 11:06:47 AM 
>> preparing matrix with flank extension from (gene_SS-500bp)~(gene_TS+500bp)... 2025-01-22 11:06:47 AM
>> 0 peaks(0%), having lengths smaller than 50bp, are filtered... 2025-01-22 11:06:47 AM
Error in cursor:(cursor + seq - 1) : result would be too long a vector

[Serine94209792]

same problem, but once you changed it to percentage, it works.

tagMatrix=getTagMatrix(peak0, windows=windows, upstream = rel(0.2), downstream = rel(0.2),nbin = 50) #make actual extension of 36bp

binning method is used...2025-01-25 17:44:48
preparing body regions by H3K4me3... 2025-01-25 17:44:48
preparing tag matrix by binning... 2025-01-25 17:44:48
preparing matrix with extension from (H3K4me3_SS-20%)~(H3K4me3_TS+20%)... 2025-01-25 17:44:48
0 peaks(0%), having lengths smaller than 50bp, are filtered... 2025-01-25 17:44:50