liftover_grlist: Liftover peak list

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Liftover peak list

Description

Perform genome build liftover to one or more GRanges objects at once.

Usage

liftover_grlist(
  grlist,
  input_build,
  output_build = "hg19",
  style = "UCSC",
  keep_chr = paste0("chr", c(seq_len(22), "X", "Y")),
  as_grangeslist = FALSE,
  merge_all = FALSE,
  verbose = TRUE
)

Arguments

grlist	A named list of GRanges objects, or simply a single unlisted GRanges object. Can perform liftover within species or across species.
input_build	The genome build of grlist.
output_build	Desired genome build for grlist to be lifted over to.
style	Chromosome style, set by seqlevelsStyle. "UCSC" : Uses the chromosome style "chr1". "NCBI" : Uses the chromosome style "1"
keep_chr	Which chromosomes to keep.
as_grangeslist	Return as a GRangesList.
merge_all	Merge all GRanges into a single GRanges object.
verbose	Print messages.

Value

Named list of lifted GRanges objects.

Examples

grlist <- list("gr1"=GenomicRanges::GRanges("4:1-100000"),
               "gr2"=GenomicRanges::GRanges("6:1-100000"),
               "gr3"=GenomicRanges::GRanges("8:1-100000"))

grlist_lifted <- liftover_grlist(grlist = grlist,
                                 input_build = "hg19",
                                 output_build="hg38")

neurogenomics/EpiCompare documentation built on April 30, 2024, 3:58 p.m.