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 1.2.0
Index]