[Bioc-sig-seq] Semantics of strandedness for gaps function

Dario Strbenac D.Strbenac at garvan.org.au
Mon Jun 28 07:30:26 CEST 2010


Hello,

I have a question that relates to the GenomicRanges vignette.

An element of the GRanges on page 9 is :

> reduce(g)
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [ 1, 7] - |
     ...    ...   ...

and the first part of the gaps() on page 10 is :

> gaps(g)
GRanges with 11 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [ 1, 249250621] + |
[2] chr1 [ 8, 249250621] - |
[3] chr1 [ 1, 249250621] * |
    ...     ...    ...

I would've thought that the gaps for the '*' strand would have the same start and end as row 2 because I had the impression that '*' means "on both strands" and there's something on the '-' strand between 1 and 7 meaning there isn't a gap "on both strands" between 1 and 7 ? It seems that gaps changes the semantics to : (NOT '+') OR (NOT '-').

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia



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