[Bioc-sig-seq] GenomicFeatures, error message

[Hervé Pagès]

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
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