Error running getBamCounts from ExomeDepth

Question

[alsanju]

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

[WouterDeCoster]

Could you print the bamlist variable?

[alsanju]

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.

[WouterDeCoster]

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

[alsanju]

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

[WouterDeCoster]

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

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

[alsanju]

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

[WouterDeCoster]

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.

[alsanju]

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.

[vincent.plagnol]

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?