MassArray (version 1.24.0)

createWiggle: Create wiggle track

Description

Function to create and write a wiggle track (UCSC Genome Browser format) to flat file from methylation data contained in a MassArrayData object

Usage

createWiggle(x, file = "", append = FALSE, colors = NULL, na.rm = FALSE, sep = " ")

Arguments

x

MassArrayData object containing methylation data for at least one sample.

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.

colors

vector of colors, indicates which colors to use for which wiggle track

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.

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

data(MassArray.example.data)
createWiggle(MassArray.example.data)