Question: biostrings report "XStringSet object is too big to be unlisted" error
gravatar for zwfanwz678
11 months ago by
zwfanwz6780 wrote:

hello everone,

I using Biostrings::readDNAStringSet to cut some sequence from hg19.fa, but an error occurs when I run the program(as follows).

seq <- Biostrings::readDNAStringSet("hg19.fa")
genome <- GenomeInfoDb::Seqinfo(genome = NA_character_)
gr_a <- BiocGenerics::unstrand(rtracklayer::import("file.bed", genome = genome))
a <- seq[gr_a]

gr_a is a GRanges object, when run a <- seq[gr_a], R report

"Error in .Call2("XStringSet_unlist", x, PACKAGE = "Biostrings") : 
  XStringSet object is too big to be unlisted (would result in an XString
  object of length 2^31 or more)"

I try these codes several times, but sometimes the code runs very well, sometimes it report the error above.

what's wrong with these code?


ADD COMMENTlink written 11 months ago by zwfanwz6780
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