breaks {VanillaICE}R Documentation

Identify breakpoints from the hidden Markov model predictions

Description

Identify breakpoints: physical position of breaks, number of SNPs in region, and the called hidden state.

Usage

breaks(x, states, position, chromosome, sampleNames, chromosomeAnnotation = NULL, verbose = FALSE)

Arguments

x Locus X sample matrix of hidden states where the hidden states are represented as integers
states Labels for the hidden states
position Physical position of loci
chromosome integer indicating chromosome (23=X)
sampleNames sample labels
chromosomeAnnotation chromosome annotation. see details
verbose verbose output

Details

One may provide their own chromosome annotation with centromere start and stop sites. The format must be the same as the chromosomeAnnotation dataset in the R package SNPchip.

Value

data.frame

sample sample label
chr chromosome (23 = X)
start starting physical position of segment
end last physical position of segment
nbases number of bases in segment
nprobes number of probes in segment
state label for the state of the segment

Author(s)

R. Scharpf

Examples

x <- matrix(rep(c(1, 2, 3, 1, 2), each=50), ncol=1)
breaks(x, states=c("0", "1", "2"), position=1:nrow(x), chromosome=1,
       sampleNames="A")

[Package VanillaICE version 1.6.0 Index]