Dear list,
I've noticed a problem counting reads using the Rsubread package. I can not include a reproducible example for lack of a bam file, but I hope the following code explains the problem:

Suppose I have this genomic region:

> regions <- data.frame(GeneID="G1", Chr="chr2", Start=202000000, End=202002100, Strand=1)

Then I want to count the reads in this region:

> featureCounts("MyReadsfile.bam", annot.ext=regions, annot.inbuilt="hg19", ignoreDup=T)

I get a huge number of reads, but if I look at the output, I see that the annotation is wrong:

$counts
      X.MyReadsfile.bam
G1                                                                       715291

$annotation
  GeneID  Chr Start       End Strand    Length
1  Error chr2     2 202002100      + 202002099

That is, the start is 2 instead of 202000000. If I print my regions I see

> regions
  GeneID  Chr    Start       End Strand
1  Error chr2 2.02e+08 202002100      1

That is, the scientific notation is not taken properly.
I can fix this doing
> par(scipen=10)

But I wanted to ask if anyone has noticed this behaviour and if this is expected by the function.

Thanks a lot for your comments,
Oscar

Oscar M. Rueda, PhD.
 Postdoctoral Research Fellow, Caldas Lab, Breast Cancer Functional
 Genomics.
 University of Cambridge. Cancer Research UK Cambridge Institute.
 Li Ka Shing Centre, Robinson Way.
 Cambridge CB2 0RE
 England


> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
 [1] Rsubread_1.14.1         GenomicAlignments_1.0.1 BSgenome_1.32.0
 [4] Rsamtools_1.16.1        Biostrings_2.32.0       XVector_0.4.0
 [7] GenomicRanges_1.16.3    GenomeInfoDb_1.0.2      IRanges_1.22.9
[10] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] BatchJobs_1.2      BBmisc_1.6         BiocParallel_0.6.1 bitops_1.0-6
 [5] brew_1.0-6         codetools_0.2-8    DBI_0.2-7          digest_0.6.4
 [9] fail_1.2           foreach_1.4.2      iterators_1.0.7    plyr_1.8.1
[13] Rcpp_0.11.2        RSQLite_0.11.4     sendmailR_1.1-2    stats4_3.1.0
[17] stringr_0.6.2      tools_3.1.0        zlibbioc_1.10.0


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