fractionAltered {snapCGH}R Documentation

Function to compute fraction of genome altered for each sample

Description

This function outputs lists containing proportions of the genome that are gained and lost for each sample.

Usage

fractionAltered(input, thres = 0.25, factor = 2.5, 
         samplenames = colnames(input$M), 
         chrominfo = chrominfo.Mb)

Arguments

input An object of type MAList or SegList
thres either a vector providing unique threshold for each sample or a vector of the same length as number of samples providing sample-specific threshold. Clone is considered to be gained if it is above the threshold and lost if it is below negative threshold. Defaults to 0.25
factor specifies the number by which experimental variability should be multiples. Used only when tumor specific variability in 'input' is not NULL or when factor is greater than 0. Defaults to 2.5.
samplenames Sample names. Default is the column names of the aCGHList object
chrominfo A chromosomal information associated with the mapping of the data. Default is chrominfo.Mb

Value

gainP Vector of proportion of genome gained for each sample
lossP Vector of proportion of genome lost for each sample

Author(s)

Jane Fridlyand, Ritu Roydasgupta


[Package snapCGH version 1.0.0 Index]