tidyChromosomes {BRGenomics} | R Documentation

## Remove odd chromosomes from GRanges objects

### Description

This convenience function removes non-standard, mitochondrial, and/or sex chromosomes from any GRanges object.

### Usage

    tidyChromosomes(
      gr,
      keep.X = TRUE,
      keep.Y = TRUE,
      keep.M = FALSE,
      keep.nonstandard = FALSE,
      genome = NULL
    )

### Arguments

`gr` | Any GRanges object, or any another object with associated `seqinfo` (or a `Seqinfo` object itself). The object should typically have a standard genome associated with it, e.g. `genome(gr) <- "hg38"`. `gr` can also be a list of such GRanges objects.
`keep.X, keep.Y, keep.M, keep.nonstandard` | Logicals indicating which non-autosomes should be kept. By default, sex chromosomes are kept, but mitochondrial and non-standard chromosomes are removed.
`genome` | An optional string that, if supplied, will be used to set the genome of `gr`.

### Details

Standard chromosomes are defined using the `standardChromosomes` function from the `GenomeInfoDb` package.

### Value

A GRanges object in which both ranges and `seqinfo` associated with trimmed chromosomes have been removed.

### Author(s)

Mike DeBerardine

### See Also

`GenomeInfoDb::standardChromosomes`

### Examples

    # make a GRanges
    chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk")
    gr <- GRanges(seqnames = chrom,
                  ranges = IRanges(start = 2*(1:6), end = 3*(1:6)),
                  strand = "+",
                  seqinfo = Seqinfo(chrom))
    genome(gr) <- "hg38"

    gr

    tidyChromosomes(gr)

    tidyChromosomes(gr, keep.M = TRUE)

    tidyChromosomes(gr, keep.M = TRUE, keep.Y = FALSE)

    tidyChromosomes(gr, keep.nonstandard = TRUE)

[Package BRGenomics version 1.0.3 Index]