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]