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.
Trying the example in section 2.7.3 of the vignette produced the following
error message:
> mmusculusEnsembl <-
+ makeTranscriptDbFromBiomart(biomart = "ensembl",
+ dataset = "mmusculus_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> rd <- RangedData(ranges = IRanges(start = c(244501,244553,244580,244523),
+ end = c(244533,244585,244612,244555)),
+ space = "chr5",
+ strand = "+")
> gr <- as(rd, "GRanges")
> transcriptsByRanges(mmusculusEnsembl, gr,
> columns=c("tx_id","tx_name","gene_id"))
GRanges with 0 ranges and 2 values columns
> grExt <- gr
> ranges(grExt) <- ranges(grExt)+100
> grExt <- reduce(grExt)
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "reduce", for signature
"GRanges"
> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-03-12 r51262)
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_0.4.1 BSgenome_1.15.12 Biostrings_2.15.23
[4] IRanges_1.5.58
loaded via a namespace (and not attached):
[1] Biobase_2.7.5 biomaRt_2.3.4 DBI_0.2-5 RCurl_1.3-1
[5] RSQLite_0.8-4 rtracklayer_1.7.10 tools_2.11.0 XML_2.6-0
>
Thanks,
P. Terry
[email protected]
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