writeWig {Repitools} | R Documentation

## 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

[Package Repitools version 1.28.0 Index]