I've been playing with mapToTranscripts(), which is a great addition BTW. It's already useful for me.

It would be nice to give a little more description in the help file on the behavior regarding the positions in the returned object and the strand of 'transcripts'. I scanned the man page and found:

"Transcriptome-based coordinates start counting at 1 at the
beginning of the ‘transcripts’ range and return positions
where ‘x’ was aligned."

But from this it was not totally obvious that 1 starts from the left regardless of the strand. E.g.:

transcripts <- GRangesList(foo=GRanges("1", IRanges(c(101,201),width=50), strand="-"))
x <- GRanges("1", IRanges(248,width=1))
mapToTranscripts(x, transcripts)
 GRanges object with 1 range and 2 metadata columns:
       seqnames    ranges strand |     xHits transcriptsHits
          <Rle> <IRanges>  <Rle> | <integer>       <integer>
   [1]      foo  [98, 98]      - |         1               1
   -------
   seqinfo: 1 sequence from an unspecified genome; no seqlengths

I believe this is not the same behavior as getSeq() for example, which would consider the rightmost position of a negative strand GRanges(List) to be position 1 in the returned DNAStringSet(List).

just to be clear, I'm not suggesting a change in behavior, just a bit more description in the man page.

R version 3.2.0 (2015-04-16)
 Platform: x86_64-apple-darwin13.4.0 (64-bit)
 Running under: OS X 10.10.3 (Yosemite)

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

 attached base packages:
  [1] splines   stats4    parallel  stats     graphics  grDevices datasets  utils     methods
 [10] base

 other attached packages:
  [1] alpine_0.1                              BiocParallel_1.2.1
  [3] speedglm_0.2-1.0                        Matrix_1.2-0
  [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 GenomicFeatures_1.20.1
  [7] AnnotationDbi_1.30.1                    Biobase_2.28.0
  [9] BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.36.0
 [11] rtracklayer_1.28.2                      GenomicAlignments_1.4.1
 [13] Rsamtools_1.20.1                        Biostrings_2.36.1
 [15] XVector_0.8.0                           GenomicRanges_1.20.3
 [17] GenomeInfoDb_1.4.0                      IRanges_2.2.1
 [19] S4Vectors_0.6.0                         BiocGenerics_0.14.0
 [21] testthat_0.9.1                          devtools_1.8.0
 [23] knitr_1.10.5                            BiocInstaller_1.18.2

 loaded via a namespace (and not attached):
  [1] Rcpp_0.11.6          compiler_3.2.0       git2r_0.10.1         futile.logger_1.4.1
  [5] bitops_1.0-6         futile.options_1.0.0 tools_3.2.0          zlibbioc_1.14.0
  [9] biomaRt_2.24.0       digest_0.6.8         memoise_0.2.1        RSQLite_1.0.0
 [13] lattice_0.20-31      DBI_0.3.1            stringr_1.0.0        roxygen2_4.1.1
 [17] rversions_1.0.0      grid_3.2.0           XML_3.98-1.1         magrittr_1.5
 [21] lambda.r_1.1.7       stringi_0.4-1        RCurl_1.95-4.6

Hi Mike,

'ignore.strand' is TRUE by default in these mapping functions. They do report position wrt strand the same as getSeq().

> mapToTranscripts(x, transcripts)
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]      foo  [98, 98]      - |         1               1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> mapToTranscripts(x, transcripts, ignore.strand=FALSE)
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     xHits transcriptsHits
         <Rle> <IRanges>  <Rle> | <integer>       <integer>
  [1]      foo    [3, 3]      - |         1               1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

We chose the default as FALSE because strand appeared to be less important (common) in RNA Seq analysis. I've added an example emphasizing the strand and a 'Note' to the arg section. Hopefully this is more clear.

Valerie