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]