readBigwig: Read a bigWig file and return it as a data frame

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

Read a bigWig file and return it as a data frame

Description

Read a bigWig file and return it as a data frame

Usage

readBigwig(
    file,
    chrom = NULL,
    chromstart = 1,
    chromend = .Machine$integer.max,
    strand = "*",
    params = NULL
)

Arguments

file	A character value specifying the path to the bigwig file.
chrom	Chromosome of data as a string, if data for a specific chromosome is desired.
chromstart	Integer start position on chromosome.
chromend	Integer end position on chromosome.
strand	A character value specifying strand. Default value is strand = "*". Options are: "+": Plus strand. "-": Minus strand. "*": Plus and minus strands.
params	An optional pgParams object containing relevant function parameters.

Details

This function does not work on Windows.

Value

Returns a 6-column dataframe of bigwig information.

See Also

import.bw

Examples

if (.Platform$OS.type != "windows"){
    bwFile <- system.file("extdata/test.bw", package="plotgardenerData")

    ## Read in entire file
    bwData <- readBigwig(file = bwFile)

    ## Read in specified region
    bwRegion <- readBigwig(file = bwFile,
                            chrom = "chr2",
                            chromstart = 1,
                            chromend = 1500)
}

PhanstielLab/BentoBox documentation built on June 30, 2024, 12:50 p.m.