[BioC] countOverlaps() only count positive strand (from GenomicRanges example)

[Vincent Carey]

On Mon, Dec 13, 2010 at 12:06 PM, Song Li <songli116 at gmail.com> wrote:
> Hi All,
>
> I was following the example in the "GenomicRanges Use Cases", section
> 3, "Simple RNA-seq Analysis", by "copy-paste" command from the
> document from page 7 to page 8:
>
> What I found out is that countOverlap() only count reads aligned to
> positive strand.  There are 28 reads map to region GRList[6645], 13 on
> positive strand, 15 on negative strand.  The "count[6645]" is 13.
>
> Is there a way to count both strand?

If you want to disregard strand of exon range, set it to "*".  This
does not appear to be a one-liner.

>
> Thanks,
> Song Li
>
> Here are all the code:
> #-----> Start with code from the package description<-------#
>> library(Rsamtools)
>> testFile <- system.file("bam", "isowt5_13e.bam", package = "leeBamViews")
>> aligns <- readBamGappedAlignments(testFile)
>> library(GenomicFeatures)
>> txdb <- makeTranscriptDbFromUCSC(genome = "sacCer2", tablename = "sgdGene")
>> exonRanges <- exonsBy(txdb, "tx")
>> length(exonRanges)
>> levels(rname(aligns)) <- c(paste("chr", as.roman(1:16),
> +     sep = ""), "chrM")
>> counts <- countOverlaps(exonRanges, aligns)
>
> #-----> find alignments that map to GRList$6645<-------#
>> aligns[705:732]
> GappedAlignments of length 28
>       rname strand cigar qwidth  start    end width ngap
> [1]  chrXIII      +   36M     36 804443 804478    36    0
> [2]  chrXIII      +   36M     36 804466 804501    36    0
> [3]  chrXIII      -   36M     36 804473 804508    36    0
> [4]  chrXIII      +   36M     36 804476 804511    36    0
> [5]  chrXIII      -   36M     36 804493 804528    36    0
> [6]  chrXIII      +   36M     36 804516 804551    36    0
> [7]  chrXIII      +   36M     36 804562 804597    36    0
> [8]  chrXIII      +   36M     36 804562 804597    36    0
> [9]  chrXIII      -   36M     36 804574 804609    36    0
> ...      ...    ...   ...    ...    ...    ...   ...  ...
> [20] chrXIII      +   36M     36 804764 804799    36    0
> [21] chrXIII      -   36M     36 804798 804833    36    0
> [22] chrXIII      +   36M     36 804799 804834    36    0
> [23] chrXIII      +   36M     36 804799 804834    36    0
> [24] chrXIII      -   36M     36 804816 804851    36    0
> [25] chrXIII      -   36M     36 804947 804982    36    0
> [26] chrXIII      -   36M     36 804953 804988    36    0
> [27] chrXIII      -   36M     36 804955 804990    36    0
> [28] chrXIII      -   36M     36 804974 805009    36    0
>> exonRanges[6646]
> GRangesList of length 1
> $6646
> GRanges with 1 range and 3 elementMetadata values
>    seqnames           ranges strand |   exon_id   exon_name exon_rank
>       <Rle>        <IRanges>  <Rle> | <integer> <character> <integer>
> [1]  chrXIII [804455, 805090]      + |      7011          NA         1
>
>
> seqlengths
>   chrIV   chrXV  chrVII  chrXII  chrXVI ...   chrVI    chrI    chrM 2micron
>  1531919 1091289 1090947 1078175  948062 ...  270148  230208   85779    6318
>> counts[6646]
> [1] 13
>> table(strand(aligns[705:732]))
>
>  +  -
> 13 15
>
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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=C              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] Rsamtools_1.2.1       Biostrings_2.18.0     GenomicFeatures_1.2.3
> [4] GenomicRanges_1.2.1   IRanges_1.8.2
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0     biomaRt_2.6.0      BSgenome_1.18.1    DBI_0.2-5
> [5] RCurl_1.4-3        RSQLite_0.9-3      rtracklayer_1.10.5 tools_2.12.0
> [9] XML_3.2-0
>
> Song Li
> --
> Postdoctoral Associate
> Institute for Genome Sciences and Policy
> Duke University
>
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