[Bioc-sig-seq] genomicFeatures, rangedData vs GRanges objects

[Hervé Pagès]

Hi,

pterry at huskers.unl.edu wrote:
>  Dear bioc-sig-sequencing,
> 
> I would like to annotate chip-seq peaks for the arabidopsis genome.  I note that GenomicFeatures (section 2.7.3 of the pdf file "Making & using TranscriptDb objects") is suggested for Chip-seq experiments.
> 
> I note a vignette dated Feb 5, 2010 uses a rangedData object, a vignette dated Feb 27, 2010 suggests a GRanges object.
> 
> My chip-seq peaks file was prepared following the handout from the 11/19/09 presentation at a Seattle workshop titled 'A ChIP-Seq Data Analysis' which on page 10 produces a rangedData object.
> 
> Testing a rangedData object as described in the Feb 5th vignette with the mmusculusEnsembl object obtained from the BioMart sec. 2.2.2 produces an error:
> 
>> rd <- RangedData(ranges = IRanges(start = c(244501,244553,244580,244523),
> +                                 end = c(244533,244585,244612,244555)),
> +                space = "chr5",
> +                strand = "+")
>> transcriptsByRanges(mmusculusEnsembl, rd, columns=c("tx_id","tx_name","gene_id"))
> Error in .txdbByRanges(txdb = txdb, ranges = ranges, restrict = match.arg(restrict),  :
>   'ranges' must be a GRanges object
>> sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-02-28 r51186)
> x86_64-unknown-linux-gnu
> 
> 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] GenomicFeatures_0.3.38 BSgenome_1.15.11       Biostrings_2.15.22
> [4] IRanges_1.5.51
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.7.4      biomaRt_2.3.4      DBI_0.2-5          RCurl_1.3-1
> [5] RSQLite_0.8-3      rtracklayer_1.7.10 tools_2.11.0       XML_2.6-0
> 
> Would you suggest I convert my rangedData object (with chip-seq peaks data)to a GRanges object?  If so, can you suggest how?  Or should I modify step(s) in the chip-seq handout to produce a GRanges object?
> 

Yep. Try 'as(rd, "GRanges")'.

Cheers,
H.


> 
> Thanks,
> P. Terry
> pterry at huskers.unl.edu
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Program in Computational Biology
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