threshold.func: Function to indicate gain or loss for each clone for each...

In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

Description

This function outputs a matrix containing gain/loss indicator for each clone and sample.

Usage

threshold.func(dat, posThres, negThres = NULL)

Arguments

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

Value

Returns a matrix with a row for each clone and column for each sample. "1" indicates gain and "-1" indicates loss.

Author(s)

Jane Fridlyand, Ritu Roydasgupta

Examples

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]

aCGH documentation built on Nov. 8, 2020, 6:58 p.m.