plotCNV: Plot CNV profiles

Description Usage Arguments

View source: R/plotCNV.R

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

1
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 Nov. 11, 2018, 5:15 a.m.