gainLoss {aCGH} | R Documentation |
This function outputs lists containing proportion of gains and losses for each clone.
gainLoss(dat, cols, thres=0.25)
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 |
gainP |
Vector of proportion gained for each clones |
lossP |
Vector of proportion lost for each clones |
Jane Fridlyand
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"))