exon.segment {DNAcopy}R Documentation

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

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.

Value

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

Author(s)

Venkatraman E. Seshan ves2111@columbia.edu

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)


[Package DNAcopy version 1.16.0 Index]