DNAcopy (version 1.46.0)

exon.segment: Binary segmentation of exon data.

Description

Compute the binary segmentation statistic, location and approximate p-value.

Usage

exon.segment(gene, eloc, edat, ngrid=100, tol=1e-6)

Arguments

gene

gene names in the exon data

eloc

exon locations within gene

edat

exon expressions within gene

ngrid

number grid points for the integral

tol

tolerance level for calculating nu

Value

a matrix with three columns. The maximal statistic from binary segmentation, its location and the p-values for each gene.

Details

The p-values are obtained by applying Siegmund's approximation for the maximal statistic from binary segmenting consecutive segments within a chromosome. These are one-sided test for an increase in expression.

Examples

# test code on an easy data set
set.seed(25)
gene <- rep(c("A", "B"), c(30,20))
eloc <- c(1:30, 1:20)
edat <- matrix(rnorm(500), 50, 10)
# changes for gene1 in samples 3 & 7
edat[1:30, 3] <- edat[1:30, 3] + rep(0.9*0:1, c(17, 13))
edat[1:30, 7] <- edat[1:30, 7] + rep(1.1*0:1, c(21, 9))
# changes for gene2 in samples 4 & 7
edat[31:50, 4] <- edat[31:50, 4] + rep(1.1*0:1, c(8, 12))
edat[31:50, 7] <- edat[31:50, 7] + rep(1.2*0:1, c(13, 7))
exon.segment(gene, eloc, edat)