easyLoad_bed: easyLoad_bed takes a character vector of file paths to bed...

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

easyLoad_bed takes a character vector of file paths to bed plus files and returning named list of GRanges.

Description

Mainly a utility function for loading MACS2 narrowPeak and broadPeak.

Usage

easyLoad_bed(
  file_paths,
  file_names = NULL,
  extraCols = character(),
  n_cores = getOption("mc.cores", 1)
)

Arguments

file_paths	character vector of paths to narrowPeak files. If named, those names will be used in output unless overriden by providing file_names.
file_names	character vector of names for output list. If not NULL will override any existing names for file_paths. Default is NULL.
extraCols	named character vector of classes. passed to rtracklayer::import for format = "BED". default is character().
n_cores	number of cores to use, uses mc.cores option if set or 1.

Value

a named list of GRanges loaded from file_paths

Examples

bed_f = system.file("extdata/test_loading.bed",
    package = "seqsetvis", mustWork = TRUE)
easyLoad_bed(bed_f, "my_bed")

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.