writeWiggle {groHMM} | R Documentation

## writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser.

### Description

writeWiggle writes a wiggle track or BigWig file suitable for uploading to the UCSC genome browser.

### Usage

    writeWiggle(reads, file, strand = "*", fileType = "wig", size = 50,
      normCounts = NULL, reverse = FALSE, seqinfo = NULL,
      track.type.line = FALSE, ...)

### Arguments

`reads` | GenomicRanges object representing the position of reads mapping in the genome.
`file` | Specifies the filename for output.
`strand` | Takes values of "+", "-", or "*". Computes Writes a wiggle on the speicified strand. "*" denotes collapsing reads on both strands. Default: "*".
`fileType` | Takes values of "wig" or "BigWig". Default: "wig".
`size` | Size of the moving window.
`normCounts` | A normalization factor correcting for library size or other effects. For example, total mappible read counts might be a reasonable value. Default: 1 (i.e. no normalization).
`reverse` | If set to TRUE, multiplies values by -1. Used for reversing GRO-seq data on the negative (-) strand. Default: FALSE
`seqinfo` | Seqinfo object for reads. Default: NULL.
`track.type.line` | If set to TRUE, prints a header identifying the file as a wiggle. Necessary to upload a custom track to the UCSC genome browser. Default: TRUE
`...` | Extra argument passed to mclapply.

### Author(s)

Minho Chae and Charles G. Danko

### Examples

    S0mR1 <- as(readGAlignments(system.file("extdata", "S0mR1.bam",
    package="groHMM")), "GRanges")
    ## Not run:
    # writeWiggle(reads=S0mR1, file="S0mR1_Plus.wig", fileType="wig",
    # strand="+", reverse=FALSE)

[Package groHMM version 1.21.0 Index]