findBreaks {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

findBreaks(x, states, position, chromosome, sample, lik1, lik2)

Arguments

x matrix of predicted hidden states (integer)
states character string giving the hidden states
position physical position of the SNPs
chromosome chromosome number
sample sample name
lik1 likelihood under alternative model
lik2 likelihood under NULL model

Value

data.frame data.frame describing regions of normal and altered states

[Package VanillaICE version 1.4.0 Index]