readBigWig: Custom bigWig reader

In JokingHero/ORFik: Open Reading Frames in Genomics

Custom bigWig reader

Description

Given 2 bigWig files (.bw, .bigWig), first is forward second is reverse. Merge them and return as GRanges object. If they contain name reverse and forward, first and second order does not matter, it will search for forward and reverse.

Usage

readBigWig(path, chrStyle = NULL, as = "GRanges")

Arguments

path	a character path to two .bigWig files, or a data.table with 2 columns, (forward, filepath) and reverse, only 1 row.
chrStyle	a GRanges object, TxDb, FaFile, , a seqlevelsStyle or Seqinfo. (Default: NULL) to get seqlevelsStyle from. In addition if it is a Seqinfo object, seqinfo will be updated. Example of seqlevelsStyle update: Is chromosome 1 called chr1 or 1, is mitocondrial chromosome called MT or chrM etc. Will use 1st seqlevel-style if more are present. Like: c("NCBI", "UCSC") -> pick "NCBI"
as	Specifies the class of the return object. Default is GRanges, which has one range per range in the file, and a score column holding the value for each range. For NumericList, one numeric vector is returned for each range in the selection argument. For RleList, there is one Rle per sequence, and that Rle spans the entire sequence.

Value

a GRanges object of the file/s

See Also

Other utils: bedToGR(), convertToOneBasedRanges(), export.bed12(), export.bigWig(), export.fstwig(), export.wiggle(), fimport(), findFa(), fread.bed(), optimizeReads(), readBam(), readWig()

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.