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Question: getSeq with GRanges object error: function not found
1
gravatar for Miskey, Csaba
4.2 years ago by
Germany
Miskey, Csaba20 wrote:

I want to retrieve genomic sequences strand specifically from hg19.
The coordinates are in a data frame, I make GRanges object out of it
and try to use getSeq.  getSeq gives me the error message below.
What's wrong?  Any alternative way?  Many thanks!

Csaba

> df <- data.frame(chr="chr1", start=11:13, end=12:14,
+                  strand=c("+","-","+"), score=1:3)
>
> gr <- makeGRangesFromDataFrame(df)
> gr
GRanges with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1  [11, 12]      +
  [2]     chr1  [12, 13]      -
  [3]     chr1  [13, 14]      +
  ---
  seqlengths:
   chr1
     NA

> getSeq(Hsapiens, gr)

Error in rep.int(DNAStringSet(""), length(sseq_idx)) : error in
  evaluating the argument 'x' in selecting a method for function
  'rep.int': Error in .Call2("new_XString_from_CHARACTER", classname,
  x, start(solved_SEW), : function '_alloc_XRaw' not provided by
  package 'IRanges'

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0                    lattice_0.20-29
[4] Biostrings_2.28.0                  GenomicRanges_1.16.4               GenomeInfoDb_1.0.2
[7] IRanges_1.22.10                    BiocGenerics_0.10.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6   grid_3.1.1     stats4_3.1.1   tools_3.1.1    XVector_0.4.0  zlibbioc_1.6.0
ADD COMMENTlink modified 4.2 years ago by Martin Morgan ♦♦ 22k • written 4.2 years ago by Miskey, Csaba20
1
gravatar for Martin Morgan
4.2 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

This looks like a package version mis-matched, try

source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocValid()

and follow the recommendations.

For a current installation of the current release, I have

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.1000 BSgenome_1.32.0                     
[3] Biostrings_2.32.1                    XVector_0.4.0                       
[5] GenomicRanges_1.16.4                 GenomeInfoDb_1.0.2                  
[7] IRanges_1.22.10                      BiocGenerics_0.10.0                 
[9] BiocInstaller_1.14.2      

Notice that we both have IRanges 1.22.10 and GenomeInfoDb 1.0.2 (both from the current release) but then your other packages are mostly from 2 Bioc releases before that.

ADD COMMENTlink written 4.2 years ago by Martin Morgan ♦♦ 22k
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