[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.
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"
Thanks for using the GRanges and GRangesList classes and providing
feedback. These classes are still very young and need to be polished.
In particular some functionalities like the "reduce" method are still
missing. I added it to GenomicRanges 0.0.4. Make sure to update your
installation in about 24 hours.
Please let us know if you run into any other problem with these
classes.
Thanks,
H.
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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--
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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