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

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Description

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

Usage

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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

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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)

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