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 ):
element AssayData to use for a given ExpressionSet input (default is "exprs") feature.chr 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 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 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 colors file cat . append na.rm sep ... 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)