[Bioc-sig-seq] GenomicFeatures, error message
Hervé Pagès
hpages at fhcrc.org
Wed Mar 17 09:51:31 CET 2010
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.
>
> 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
> pterry at huskers.unl.edu
>
> [[alternative HTML version deleted]]
>
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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: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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