Question: CHIPseeker error now
0
gravatar for lzhizhao9179
11 months ago by
lzhizhao91790 wrote:
tagMatrix_1 <- getTagMatrix(peak_1, weightCol =NULL, windows = promoter_1)
Error in split.default(1:length(windows), as.factor(seqnames(windows))) : 
  group length is 0 but data length > 0
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
  
R • 378 views
ADD COMMENTlink modified 11 months ago by zx87548.0k • written 11 months ago by lzhizhao91790

It is a good idea to Google your error/warning messages, if you did the search then you would see that there is an issue at GitHub with a solution.

Seems like the problem was the chromosome column being labelled (1 instead of chr1)

Fixed with:

newStyle <- mapSeqlevels(seqlevels(peak), "UCSC")
peakchr <- renameSeqlevels(peak, newStyle)
ADD REPLYlink written 11 months ago by zx87548.0k
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