writeWig: Writes sequencing data out into wiggle files

Description Usage Arguments Details Value Author(s) Examples

Description

Writes sequencing data out into wiggle files

Usage

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  ## 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

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#See examples in the manual

Repitools documentation built on Nov. 17, 2017, 12:46 p.m.