Filters unwanted seqlevels from a Genomic Ranges object or similar object

This function allows for removal of manually designated or more broadly undesirable seqlevels from a Genomic Ranges object or similar object

filterChrGR(
  gr = NULL,
  remove = NULL,
  underscore = TRUE,
  standard = TRUE,
  pruningMode = "coarse"
)

Arguments

gr

A GRanges object or another object containing seqlevels.

remove

A character vector indicating the seqlevels that should be removed if manual removal is desired for certain seqlevels. If no manual removal is desired, remove should be set to NULL.

underscore

A boolean value indicating whether to remove all seqlevels whose names contain an underscore (for example "chr11_KI270721v1_random").

standard

A boolean value indicating whether only standard chromosomes should be kept. Standard chromosomes are defined by GenomeInfoDb::keepStandardChromosomes().

pruningMode

The name of the pruning method to use (fromGenomeInfoDb::seqinfo()) when seqlevels must be removed from a GRanges object. When some of the seqlevels to drop from the given GRanges object are in use (i.e. have ranges on them), the ranges on these sequences need to be removed before the seqlevels can be dropped. Four pruning modes are currently defined: "error", "coarse", "fine", and "tidy".