plotCNV: Plot CNV profiles

In PietaSchofield/plibb: Pieta Schofield's repository of former useful R functions

Description

There are 6 states, which in a diploid sample corresponds to the following chromosomal copies and biological state: 1 <= 0 copies, homozogous deletion 2 == 1 copy, heterozogous deletion 3 == 2 copies, neutral 4 == 3 copies, gain 5 == 4 copies, amplification 6 >= 5 copies, high level amplification Output: states - The state assigned to each copy number value segs - Non-overlapping segments and medians of each segment mus - Optimal median of of copy numbers in state lambda - Optimal precision of copy numbers in state pi - Optimal state distribution loglik - The likelihood values of each EM algorithm iteration rho - Posterior marginals (responsibilities) for each position and state

Usage

plotCNV(copyData, segData, paramList, reduceCol = T)

Arguments

copyData	list of RangedData Objects with copy number
segData	list of corresponding segmentation data
param	list of initial parameter

PietaSchofield/plibb documentation built on May 6, 2019, 6:45 p.m.