gainLoss: Function to compute proportion of gains and losses for each...

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
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"))

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