drighelli / descan2 Goto Github PK

When providing a list of peaks without the "k-carriers" colname, it filters out these peaks.

Possible solution: Provide a workaround behaviour with an argument for the user and produce a message in the verbose

Create a function that is able to compute z-score n-peaks k-carriers from the output of ChIPpeakAnno::findOverlapsOfPeaks function

Hi,

I wanted to test DEScan2 on hg38 aligned bam files, however it does not seem to work at the countFinalRegions step:

finalRegions <- DEScan2::countFinalRegions(regionsGRanges=regionsGR, readsFilePath=bam.files, fileType="bam", minCarriers=1,genomeName="hg38", onlyStdChrs=TRUE, saveFlag=FALSE,verbose=FALSE) 

Error in setGRGenomeInfo(GRanges = regionsGRanges, genomeName = genomeName) :
  Cannot find the  in genome hg38 Maybe a problem of chromosome labels

How can I resolve this?

Error generated in findOverlapsOverSamples from findOverlapsOfPeaks which removes the score column from the peaksInMergedPeaks.

In order to rescue the scores it'd sufficient to retrieve the names and get the single scores from each peak group (gri and grj)

when creating summarized experiment use:

summarizedExperiment(assays=list(counts=countMatrix, etc)

• When I call DEScan2::findPeaks with genomeName="mm10", I get the following error:

Get seqlengths from genome mm10
Error in value[3L] :
Unable to retrieve the genome mm10 returned: Error in .order_seqlevels(chrom_sizes[, "chrom"]): !anyNA(m31) is not TRUE

• The alternative reference genomeName="GRCm38" seems to be retrieved but this annotation's seqnames don't have the prefix "chr", so it fails at the seqname check ("Maybe a problem of chromosome labels").