createWiggle: Create wiggle track

Description Usage Arguments Author(s) References See Also Examples

Description

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

Usage

1

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.

\dots

other arguments to be passed to cat. See cat.

Author(s)

Reid F. Thompson ([email protected])

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

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#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)

HELP documentation built on May 2, 2018, 2:28 a.m.