exon.segment {DNAcopy} | R Documentation |
Compute the binary segmentation statistic, location and approximate p-value.
exon.segment(gene, eloc, edat, ngrid=100, tol=1e-6)
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 |
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.
a matrix with three columns. The maximal statistic from binary segmentation, its location and the p-values for each gene.
Venkatraman E. Seshan ves2111@columbia.edu
# 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)