| createWiggle {HELP} | R Documentation |
Create and write a wiggle track (UCSC Genome Browser format) to flat file
createWiggle(x, y, ...)
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):
elementAssayData to use for a given ExpressionSet input (default is "exprs") feature.chrfeatureData to use as chromosomal information (default is "CHR"). Can be a character matching varLabel or simply an integer indicating which feature to choose. feature.startfeatureData to use as start positions (default is "START"). Can be a character matching varLabel or simply an integer indicating which feature to choose. feature.stopfeatureData to use as end positions (default is "STOP"). Can be a character matching varLabel or simply an integer indicating which feature to choose. samplescolorsfilecat. appendna.rmsep...cat. See cat. |
Reid F. Thompson (rthompso@aecom.yu.edu)
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).
#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)