exon.segment: Binary segmentation of exon data.

In veseshan/DNAcopy: DNA Copy Number Data Analysis

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

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)

veseshan/DNAcopy documentation built on Oct. 18, 2023, 8:30 p.m.