You can readGappedAlignments to load the file as a GappedAlignments. Then
call coverage() on that.

Michael

On Tue, Jul 17, 2012 at 12:56 PM, Rithun Mukherjee [guest] <
guest@bioconductor.org> wrote:

>
> I am trying to obtain per reference base position coverage for a BAM file.
> The BAM file has been generated by Samtools and contains alignment info for
> 10 million reads to a 7kb reference plasmid genome. What is the best way to
> go about this? I have explored the "readBamGappedAlignments" and
> "readAligned" functions but I am not sure of the way forward from there.
>
> Also should I be using a BAM file or the sorted BAM file with its
> corresponding index file? I am currently using the later.
>
> Thanks much.
>
>
>  -- output of sessionInfo():
>
> R version 2.14.2 (2012-02-29)
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 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] ShortRead_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5
> [4] lattice_0.20-6      Rsamtools_1.6.3     Biostrings_2.22.0
> [7] GenomicRanges_1.6.7 IRanges_1.12.6
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    grid_2.14.2
>  [5] hwriter_1.3        RCurl_1.91-1       rtracklayer_1.14.4 tools_2.14.2
>  [9] XML_3.9-4          zlibbioc_1.0.1
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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