CoverageView package_Error in 1:nrow(grDF) : argument of length 0
Hi,
I am trying to use cov.matrix() from CoverageView package and getting following error:
>mybed <- read.table("mybed.bed", sep='\t', header = FALSE)
>mybed
V1 V2 V3 V4 V5 V6
1 chr1 468 558 AMPL1 strand gene1
2 chr1 1558 1609 AMPL2 strand gene2
3 chr1 3768 3817 AMPL3 strand gene3
4 chr3 10 59 AMPL4 strand gene3
5 chr3 1067 1128 AMPL5 strand gene4
>trm <- CoverageBamFile("mybam.bam", reads_mapped=11906)
>trm
class: CoverageBamFile
path: mybam.bam
index: mybam.bam.bai
isOpen: FALSE
yieldSize: NA
obeyQname: FALSE
asMates: FALSE
qnamePrefixEnd: NA
qnameSuffixStart: NA
reads_mapped: 11906
run_type: single
>df <- cov.matrix(trm, coordfile = mybed, ctl = NULL, extend = 10, num_cores=1)
[INFO] A coverage matrix will be generated by calculating the 'log2ratio' of the coverages.
[INFO] processing:mybam.bam
Error in 1:nrow(grDF) : argument of length 0
>traceback()
4: lapply(X, FUN, ...)
3: mclapply(1:nrow(grDF), loopfun, mc.cores = num_cores, obj = tr)
2: cov.matrix(trm, coordfile = mybed, ctl = NULL, extend = 10, num_cores = 1)
1: cov.matrix(trm, coordfile = mybed, ctl = NULL, extend = 10, num_cores = 1)
Kindly guide.
Thanks!
1 answer
I had the same issue, but for me it worked when I specified the path to the bed file instead of the object to which I have saved it in before. Try:
>df <- cov.matrix(trm, coordfile = "mybed.bed", ctl = NULL, extend = 10, num_cores=1)
instead of
>df <- cov.matrix(trm, coordfile = mybed, ctl = NULL, extend = 10, num_cores=1)
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