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