readWig: Custom wig reader

In JokingHero/ORFik: Open Reading Frames in Genomics

Custom wig reader

Description

Given 2 wig files, 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

readWig(path, chrStyle = NULL)

Arguments

path	a character path to two .wig 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"

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(), readBigWig()

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