writeWig: Writes sequencing data out into wiggle files

In markrobinsonuzh/Repitools: Epigenomic tools

Writes sequencing data out into wiggle files

Description

Writes sequencing data out into wiggle files

Usage

  ## S4 method for signature 'AffymetrixCelSet'
writeWig(rs, design=NULL, log2.adj=TRUE, verbose=TRUE)
  ## S4 method for signature 'GRangesList'
writeWig(rs, seq.len = NULL, design=NULL, sample=20, drop.zero=TRUE, normalize=TRUE, verbose=TRUE)

Arguments

rs	The sequencing or array data.
design	design matrix specifying the contrast to compute (i.e. the samples to use and what differences to take)
log2.adj	whether to take log2 of array intensities.
verbose	Whether to write progress to screen
seq.len	If sequencing reads need to be extended, the fragment size to be used
sample	At what basepair resolution to sample the genome at
drop.zero	Whether to write zero values to the wiggle file - TRUE saves diskspace
normalize	Whether to normalize each lane to its total number of reads, TRUE is suggested

Details

A wiggle file is created for each column in the design matrix (if design is left as NULL, then a file is created for each array/lane of sequencing). The filenames are given by the column names of the design matrix, and if ending in "gz" will be written out as a gzfile.

Value

Wiggle file(s) are created

Author(s)

Aaron Statham

Examples

#See examples in the manual

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.