Question: aroundPromoter function in RiboSeqR gives error
0
gravatar for amir.mahboubi.79
7 months ago by
amir.mahboubi.790 wrote:

Hi,

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:

#Install

source("http://bioconductor.org/biocLite.R")

#Load the library

library(RiboProfiling)

#BAM file import

library(GenomicAlignments)

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

#txdb object with annotations

biocLite("TxDb.Athaliana.BioMart.plantsmart28")

library(TxDb.Athaliana.BioMart.plantsmart28)

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?

 

Thanks

Amir Mahboubi

Postdoc at Umea plant science centre

Umea, Sweden

riboseqr • 147 views
ADD COMMENTlink written 7 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 7 months ago • written 7 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 4 months ago • written 5 months ago by ahowells0
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