createWiggle {HELP} | R Documentation

## Create wiggle track

### Description

Create and write a wiggle track (UCSC Genome Browser format) to flat file

### Usage

    createWiggle(x, y, ...)

### Arguments

`x` | matrix of numerical data, where each column represents data for an individual wiggle track. `x` can also be of class `"ExpressionSet"`.
`y` | an additional matrix of numerical data with columns corresponding to chr, start, and end, respectively.
`...` | Arguments to be passed to methods (see `createWiggle-methods`): `element` which element of `AssayData` to use for a given `ExpressionSet` input (default is "exprs") `feature.chr` which element of `featureData` to use as chromosomal information (default is "CHR"). Can be a character matching `varLabel` or simply an integer indicating which feature to choose. `feature.start` which element of `featureData` to use as start positions (default is "START"). Can be a character matching `varLabel` or simply an integer indicating which feature to choose. `feature.stop` which element of `featureData` to use as end positions (default is "STOP"). Can be a character matching `varLabel` or simply an integer indicating which feature to choose. `samples` which sample(s) to use as data. Can be a vector of characters matching sample names, integers indicating which samples to choose, or a mixture of the two. If NULL (default), all samples will be used. `colors` vector of colors, indicates which colors to use for which wiggle track `file` location of file to write wiggle track information; if "", wiggle track prints to the standard output connection: see `cat`. `append` logical; if TRUE, the output is appended to an existent wiggle track file. If FALSE (default), a new file with a new header is created and any existing file of the same name is destroyed. `na.rm` logical; if TRUE (default), missing values are removed from data. If FALSE any missing values cause an error `sep` a string used to separate columns. Using sep = "t" (default) gives tab-delimited output. `...` other arguments to be passed to `cat`. See `cat`.

### Author(s)

Reid F. Thompson (rthompso@aecom.yu.edu)

### References

UCSC Genome Browser, http://genome.ucsc.edu/goldenPath/help/customTrack.html: Kent, W.J., Sugnet, C. W., Furey, T. S., Roskin, K.M., Pringle, T. H., Zahler, A. M., and Haussler, D. The Human Genome Browser at UCSC. Genome Res. 12(6), 996-1006 (2002).

### See Also

`write`, `cat`

### Examples

    #demo(pipeline,package="HELP")

    chr <- rep("chr1", 500)
    start <- (1:500)*200
    end <- start+199
    data <- sample(5*(1:10000/10000)-2, size=500)
    data <- cbind(data, abs(data), -1*data)
    colnames(data) <- c("data", "abs", "opposite")
    createWiggle(data, cbind(chr, start, end))

    #rm(chr, start, end, data)

[Package HELP version 1.0.0 Index]