threshold.func {aCGH} | R Documentation |
This function outputs a matrix containing gain/loss indicator for each clone and sample.
threshold.func(dat, posThres, negThres = NULL)
dat |
log2ratios of the relevant array CGH object |
posThres |
Global or sample-specific threshold for gain |
negThres |
Global or sample-specific threshold for loss. Defaults to -posThres |
Returns a matrix with a row for each clone and column for each sample. "1" indicates gain and "-1" indicates loss.
Jane Fridlyand, Ritu Roydasgupta
data(colorectal) factor <- 3 tbl <- threshold.func(log2.ratios(colorectal),posThres=factor*(sd.samples(colorectal)$madGenome)) rownames(tbl) <- clone.names(colorectal) colnames(tbl) <- sample.names(colorectal) tbl[1:5,1:5]