Question: aroundPromoter function in RiboSeqR gives error
gravatar for amir.mahboubi.79
13 months ago by
amir.mahboubi.790 wrote:


I am performing RiboseqR analysis now and ran into a problem with aroundPromoter command that I don't understand and have no idea what to do. The problem is that when I run my command as below:



#Load the library


#BAM file import


aln <- readGAlignments(BamFile("/Users/amir/Documents/Amir files/iSeq 100 data/Iseq data analyzed/‌bam files/BAM_4D-Suc.bam"))

#txdb object with annotations



txdb <- TxDb.Athaliana.BioMart.plantsmart28

oneBinRanges <- aroundPromoter(txdb, alnGRanges, percBestExpressed=0.001)


I then get the error:


Error in if (quantCounts <= 0) { : missing value where TRUE/FALSE needed


Can you please help me what should I do to get rid of this problem?



Amir Mahboubi

Postdoc at Umea plant science centre

Umea, Sweden

riboseqr • 206 views
ADD COMMENTlink written 13 months ago by amir.mahboubi.790

I have exact same problem analyzing footprints from mouse liver. Any insight would be much appreciated.

ADD REPLYlink modified 12 months ago • written 12 months ago by RiboIN0

Hi everyone! I am also running into the same error message with the aroundPromoter function. Any progress? Has anyone been successful in contacting the researchers maintaining this package? Thank you!

ADD REPLYlink modified 10 months ago • written 10 months ago by ahowells0
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