 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?


Thanks,
P. Terry
pterry@huskers.unl.edu

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