Hi,
[email protected] 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
[email protected]
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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