[BioC] export funciton alters ranges in output BED file

[do r]

Hello

I am attempting to use the export() function to generate a BED file from a
GRanges object.
However, the ranges in the output file are altered so that the start
coordinate is subtracted by one,
for example:

[987]        3 [37035154, 37035155]      +   |  Class 4     MLH1    c.116+1G>A
  [988]        3 [37067241, 37067242]      +   |  Class 4     MLH1     c.1153C>T
  [989]        3 [37067125, 37067126]      +   |  Class 4     MLH1   c.1039-2A>T
  [990]        3 [37067125, 37067126]      +   |  Class 4     MLH1   c.1039-2A>G
  [991]        3 [37061954, 37061955]      +   |  Class 4     MLH1   c.1038+1G>C

results in this output:
3	37067240	37067242	.	0	+
3	37067124	37067126	.	0	+
3	37067124	37067126	.	0	+
3	37061953	37061955	.	0	+

Since I intend to later to searrch for intersections between the
ranges in the BED file and variants in a vcf file (using Tabix), I am
afraid that this subtratcion may lead to false positive.

What is the reason for this subtraction from the start and is there
any way to supress it?

thanks in advance

Dolev Rahat


sessionInfo:

R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] rtracklayer_1.24.2   GenomicRanges_1.16.4 GenomeInfoDb_1.0.2
IRanges_1.22.10      BiocGenerics_0.10.0
[6] BiocInstaller_1.14.2 stringr_0.6.2

loaded via a namespace (and not attached):
 [1] BatchJobs_1.3           BBmisc_1.7
BiocParallel_0.6.1      Biostrings_2.32.1
 [5] bitops_1.0-6            brew_1.0-6              BSgenome_1.32.0
      checkmate_1.4
 [9] codetools_0.2-9         DBI_0.3.0               digest_0.6.4
      fail_1.2
[13] foreach_1.4.2           GenomicAlignments_1.0.6 iterators_1.0.7
      Rcpp_0.11.2
[17] RCurl_1.95-4.3          Rsamtools_1.16.1        RSQLite_0.11.4
      sendmailR_1.1-2
[21] stats4_3.1.0            tools_3.1.0             XML_3.98-1.1
      XVector_0.4.0
[25] zlibbioc_1.10.0

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