import-functions: Import basepair-resolution files

In mdeber/BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Import basepair-resolution files

Description

Import functions for plus/minus pairs of bigWig or bedGraph files.

Usage

import_bigWig(
  plus_file = NULL,
  minus_file = NULL,
  genome = NULL,
  keep.X = TRUE,
  keep.Y = TRUE,
  keep.M = FALSE,
  keep.nonstandard = FALSE,
  makeBRG = TRUE,
  ncores = getOption("mc.cores", 2L)
)

import_bedGraph(
  plus_file = NULL,
  minus_file = NULL,
  genome = NULL,
  keep.X = TRUE,
  keep.Y = TRUE,
  keep.M = FALSE,
  keep.nonstandard = FALSE,
  ncores = getOption("mc.cores", 2L)
)

Arguments

plus_file, minus_file	Paths for strand-specific input files, or a vector of such paths. If vectors are given, the user should take care that the orders match!
genome	Optional string for UCSC reference genome, e.g. "hg38". If given, non-standard chromosomes are trimmed, and options for sex and mitochondrial chromosomes are applied.
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.
makeBRG	If TRUE (the default), the output ranges are made single-width using makeGRangesBRG
ncores	Number of cores to use, if importing multiple objects simultaneously.

Details

For import_bigWig, the output GRanges is formatted by makeGRangesBRG, such that all ranges are disjoint and have width = 1, and the score is single-base coverage, i.e. the number of reads for each position.

import_bedGraph is useful for when both 5'- and 3'-end information is to be maintained for each sequenced molecule. For this purpose, one use bedGraphs to store entire reads, with the score representing the number of reads sharing identical 5' and 3' ends. However, import_bedGraph doesn't modify the information in the bedGraph files. If the bedGraph file represents basepair-resolution coverage data, then users can coerce it to a basepair-resolution GRanges object by using getStrandedCoverage followed by makeGRangesBRG.

Value

Imports a GRanges object containing base-pair resolution data, with the score metadata column indicating the number of reads represented by each range.

Author(s)

Mike DeBerardine

See Also

tidyChromosomes, rtracklayer::import.bw, rtracklayer::import.bedGraph

Examples

#--------------------------------------------------#
# Import PRO-seq bigWigs -> coverage of 3' bases
#--------------------------------------------------#

# get local address for included bigWig files
p.bw <- system.file("extdata", "PROseq_dm6_chr4_plus.bw",
                    package = "BRGenomics")
m.bw <- system.file("extdata", "PROseq_dm6_chr4_minus.bw",
                    package = "BRGenomics")

# import bigWigs (not supported on windows)
if (.Platform$OS.type == "unix") {
    PROseq <- import_bigWig(p.bw, m.bw, genome = "dm6")
    PROseq
}


#--------------------------------------------------#
# Import PRO-seq bedGraphs -> whole reads (matched 5' and 3' ends)
#--------------------------------------------------#

# get local address for included bedGraph files
p.bg <- system.file("extdata", "PROseq_dm6_chr4_plus.bedGraph",
                    package = "BRGenomics")
m.bg <- system.file("extdata", "PROseq_dm6_chr4_minus.bedGraph",
                    package = "BRGenomics")

# import bedGraphs
PROseq_paired <- import_bedGraph(p.bg, m.bg, genome = "dm6")
PROseq_paired

mdeber/BRGenomics documentation built on Aug. 3, 2024, 3:43 a.m.