Question

How to remove aberrant chromosomes from a BSgenome object?

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tlgolan • 0

@tlgolan-10804

Last seen 8.3 years ago

Hi everyone,

How can I remove mitochondrial chromosome and aberrant chromosomes ("_" pattern) from a BSgenome object? I am trying to create such object that contains only chr1-20 and X,Y chromosomes (Rn6 genome).

Thanks!

bsgenome r • 3.3k views

ADD COMMENT • link updated 8.5 years ago by Hervé Pagès 16k • written 8.5 years ago by tlgolan • 0

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Hi

Depending on what you want to do, subsetting might help, eg:

seqinfo(BSgenome.Rnorvegicus.UCSC.rn6)[seqlevels(BSgenome.Rnorvegicus.UCSC.rn6)[1:22]]

getSeq(BSgenome.Rnorvegicus.UCSC.rn6, seqlevels(BSgenome.Rnorvegicus.UCSC.rn6)[1:22])

Regards, Hans-Rudolf

ADD REPLY • link 8.5 years ago Hotz, Hans-Rudolf ▴ 400

score 2 · Answer 1 · 2016-06-11

Hi,

Unfortunately the seqlevels() setter for BSgenome objects only allows renaming the sequences at the moment. It doesn't allow removing sequences. It should at some point (it's on the TODO list). Here is a hack in the mean time:

keepBSgenomeSequences <- function(genome, seqnames)
{
    stopifnot(all(seqnames %in% seqnames(genome)))
    genome@user_seqnames <- setNames(seqnames, seqnames)
    genome@seqinfo <- genome@seqinfo[seqnames]
    genome
}

Then:

library(BSgenome.Rnorvegicus.UCSC.rn6)
genome <- BSgenome.Rnorvegicus.UCSC.rn6
sequences_to_keep <- paste0("chr", c(1:20, "X", "Y"))
genome <- keepBSgenomeSequences(genome, sequences_to_keep)
genome
# Rat genome:
## organism: Rattus norvegicus (Rat)
## provider: UCSC
## provider version: rn6
## release date: Jul. 2014
## release name: RGSC Rnor_6.0
## 22 sequences:
##   chr1  chr2  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chr10 chr11 chr12
##   chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chrX  chrY             
## (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
## to access a given sequence)

Hope this helps,

H.