gainLoss {aCGH} | R Documentation

## Function to compute proportion of gains and losses for each clones

### Description

This function outputs lists containing proportion of gains and losses for each clone.

### Usage

    gainLoss(dat, cols, thres=0.25)

### Arguments

`dat` | log2ratios of the relevant array CGH object
`cols` | indeces of the samples to use
`thres` | global or tumor-specific threshold. defaults to 0.25

### Value

`gainP` | Vector of proportion gained for each clones
`lossP` | Vector of proportion lost for each clones

### Author(s)

Jane Fridlyand

### See Also

`plotFreqStat`

### Examples

    data(colorectal)

    ## Use mt.maxT function from multtest package to test
    ## differences in group means for each clone grouped by sex
    ##use only clones with show gain or loss in at least 10% of the samples
    colnames(phenotype(colorectal))
    sex <- phenotype(colorectal)$sex
    sex.na <- !is.na(sex)
    colorectal.na <- colorectal[ ,sex.na, keep = TRUE ]
    factor <- 2.5
    minChanged <- 0.1
    gainloss <- gainLoss(log2.ratios(colorectal.na), cols=1:ncol(colorectal.na), thres=factor*sd.samples(colorectal.na)$madGenome)
    ind.clones.use <- which(gainloss$gainP >= minChanged | gainloss$lossP>= minChanged)
    #create filtered dataset
    colorectal.na <- colorectal.na[ind.clones.use,keep=TRUE]
    dat <- log2.ratios.imputed(colorectal.na)
    resT.sex <- mt.maxT(dat, sex[sex.na],test = "t.equalvar", B = 1000)

    ## Plot the result along the genome
    plotFreqStat(colorectal.na, resT.sex, sex[sex.na],factor=factor,titles = c("Male", "Female"))

[Package aCGH version 1.66.0 Index]