Drop non-standard chromosomes

Drop non-standard chromosomes

pruningSequences(genesList, negativePattern = "[_.M]")

Arguments

genesList

A list of GRanges object

negativePattern

The pattern to match the seqnames that does not need.

Value

A list of filtered GRanges

Examples

library(GenomicRanges)
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: 'generics'
#> The following objects are masked from 'package:base':
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))
pruningSequences(list(gr))
#> [[1]]
#> GRanges object with 4 ranges and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr2      1-10      *
#>   [2]     chr3      2-10      *
#>   [3]     chr2      4-10      *
#>   [4]     chr3      5-10      *
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
#>