Question: Error running getBamCounts from ExomeDepth
0
gravatar for alsanju
2.8 years ago by
alsanju0
Spain
alsanju0 wrote:

Hi all, I have a problem when running Exomedepth when executing getBamCounts:

> require(ExomeDepth) 

> data(exons.hg19) 

> options(stringsAsFactors=FALSE)

> bamlist = read.table('bam.list')$V1 

> counts = getBamCounts(bed.frame = exons.hg19, bam.files = bamlist)

The output error is:

Error in as.vector(x, mode) :
  '.SigArgs' is shorter than '.SigLength' says it should be

> sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ExomeDepth_1.1.10 optparse_1.3.2

loaded via a namespace (and not attached):
 [1] lattice_0.20-24            IRanges_2.8.1
 [3] Rsamtools_1.26.1           Biostrings_2.42.0
 [5] bitops_1.0-6               GenomicAlignments_1.10.0
 [7] grid_3.3.2                 GenomeInfoDb_1.10.1
 [9] stats4_3.3.2               zlibbioc_1.20.0
[11] XVector_0.14.0             getopt_1.20.0
[13] S4Vectors_0.12.0           Matrix_1.1-2
[15] aod_1.3                    BiocParallel_1.8.1
[17] tools_3.3.2                Biobase_2.34.0
[19] parallel_3.3.2             BiocGenerics_0.20.0
[21] GenomicRanges_1.26.1       SummarizedExperiment_1.4.0
R cnv exomedepth • 1.5k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by alsanju0

Could you print the bamlist variable?

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

The bamlist variable looks like this

str(bamlist)
chr [1:23] "file1.bam" "file2.bam" "file3.bam"

The vignette says that bam.files argument has to be "character, list of BAM files to extract read count data from". I have also tried using a list, but it still not working.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by alsanju0

Is the chromosome notation in your bam files the same as in exons.hg19?

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

Both bam files have the chromosome notation without 'chr', e.g. "1", "2"...

ADD REPLYlink written 2.8 years ago by alsanju0

And you bamfiles are indexed, i.e. file1.bam.bai?

(If this doesn't explain it I have no idea what's wrong)

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

Yes, they are indexed in the same dir than the bam files are located as fileX.bam.bai

ADD REPLYlink written 2.8 years ago by alsanju0

Well I'm out of ideas, you could try traceback() after getting the error to trace the error. Besides that, perhaps your best guess is contacting the author of the package.

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

The traceback() output is:

17: as.vector(x, mode)

16: as.vector(x, mode = "integer")

15: .local(x, ...)

14: as.integer(seqnames(x))

13: as.integer(seqnames(x))

12: get_out_of_bound_index(x)

11: valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE)

10: valid.func(object)

9: validityMethod(as(object, superClass))

8: anyStrings(validityMethod(as(object, superClass)))

7: validObject(.Object)

6: initialize(value, ...)

5: initialize(value, ...)

4: new(Class, seqnames = seqnames, ranges = ranges, strand = strand, elementMetadata = mcols, seqinfo = seqinfo)

3: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges, strand = strand, mcols = mcols, seqlengths = seqlengths, seqinfo = seqinfo)

2: GenomicRanges::GRanges(seqnames = bed.frame$seqnames, IRanges::IRanges(start = bed.frame$start + 1, end = bed.frame$end))

1: getBamCounts(bed.frame = exons.hg19, bam.files = bamlist)

Anyway, I am contacting the author of the package. Thanks for replying.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by alsanju0

Well I am not sure. Definitely something to do with the chromosome names, as it's a seqnames pbm. What reference genome did you use exactly?

ADD REPLYlink written 2.8 years ago by vincent.plagnol20
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