[Bioc-sig-seq] extract 3UTR using GenomicFeatures package

[Pages, Herve]

Hi Jason,

Thanks for the report! This is now fixed in GenomicFeatures 1.3.15.

  > library(GenomicFeatures)
  > txdb <- loadFeatures("txdb.hg19.refGene.sqlite")
  > threeutr.tx <- threeUTRsByTranscript(txdb, use.names=TRUE)
  > library(BSgenome.Hsapiens.UCSC.hg19)
  > extractTranscriptsFromGenome(Hsapiens, threeutr.tx[1:4])
    A DNAStringSet instance of length 4
      width seq                                               names               
  [1]  1990 TGAAATCTTATGCAAGGATTTGG...ATATTAAAAACATGTAAATATTA NM_032291
  [2]  1093 ATCTCTCCTCTCCTCCTTGTCTG...TTACTTCTGTCATTGTATGTGAA NM_001145277
  [3]   212 GTGGGCCTCGTTCCCCCCGGAGA...CAACATAAATCCTGTTCCTTCCA NM_052998
  [4]  1199 CCTGAGCACGGTTTTTCCTCATG...TTACTTCTGTCATTGTATGTGAA NM_001145278

It was an sapply() used internally when an lapply() should have been
used. It didn't make any difference so far because the supplied
GRangesList object would typically have top-level elements of variable
length, but in your case they are all of length 1.

GenomicFeatures 1.3.15 should become available thru biocLite() in the
next 24 hours or so.

Cheers,
H.


----- Original Message -----
From: "Jason Lu" <jasonlu68 at gmail.com>
To: bioc-sig-sequencing at r-project.org
Sent: Wednesday, March 16, 2011 1:57:06 PM
Subject: [Bioc-sig-seq] extract 3UTR using GenomicFeatures package

Hi,

I would like to extract 3'UTR for a list of refseq NMs using the
GenomicFeatures pkg.  However I encountered the following error.

Here is what I have:

===================
library(GenomicFeatures)
txdb  = loadFeatures("txdb.hg19.refGene.sqlite")
threeutr.tx = threeUTRsByTranscript(txdb, use.names=TRUE)


library("BSgenome.Hsapiens.UCSC.hg19")
> extractTranscriptsFromGenome(Hsapiens,threeutr.tx[1:4])
Error in .normargExonStartsOrEnds(exonStarts, "exonStarts") :
  'exonStarts' must be a list of integer vectors, an IntegerList object,
  or a character vector where each element is a comma-separated list of
  integers

> sessionInfo()
R version 2.13.0 Under development (unstable) (2011-01-20 r54055)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] GenomicFeatures_1.3.14             BSgenome.Hsapiens.UCSC.hg19_1.3.17
[3] BSgenome_1.19.5                    Biostrings_2.19.17
[5] GenomicRanges_1.3.25               IRanges_1.9.27

loaded via a namespace (and not attached):
[1] Biobase_2.11.10     DBI_0.2-5           RCurl_1.5-0
[4] RSQLite_0.9-4       XML_3.2-0           biomaRt_2.7.1
[7] rtracklayer_1.11.12 tools_2.13.0


Thanks for checking.

Jason

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