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!

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.