[BioC] package Genominator with ShortRead-annotation question

[Kasper Daniel Hansen]

Nitzan,

You are talking about the annotation data.frame?  Yes, you need the
chromosome names to be integers.  If you have a chromosome map you can
fix this by

anno$chr <- match(anno$old_chr, chrMap)

Kasper

On Thu, Nov 17, 2011 at 4:10 AM, nitzan kol [guest]
<guest at bioconductor.org> wrote:
>
> in the simple annotation objects chr entries should be the original chr numbers or indices into chrMap?
> in your withShortRead example THRO55C.1 had VIII translated to 8 in the simple annotation form when in chrMap it has location 13 in chrMap.
>
>  thank you
> Nitzan
>
>  -- output of sessionInfo():
>
> R version 2.11.0 (2010-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] Genominator_1.2.0   GenomeGraphs_1.8.0  biomaRt_2.4.0
>  [4] RSQLite_0.9-1       DBI_0.2-5           ShortRead_1.6.2
>  [7] Rsamtools_1.0.8     lattice_0.18-5      Biostrings_2.16.9
> [10] GenomicRanges_1.0.9 IRanges_1.6.17
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 hwriter_1.3   RCurl_1.6-10  tools_2.11.0  XML_3.4-3
>
> --
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>
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