copynumberEmission {VanillaICE}R Documentation

Emission probabilities for copy number

Description

Emission probabilities for copy number

Usage

copynumberEmission(copynumber, states, mu, sds, takeLog, verbose = TRUE,
na.rm=TRUE)

Arguments

copynumber matrix
states character string
mu numeric: mean of hidden states for Gaussian
sds standard deviations of copy number estimates
takeLog logical: if TRUE, this function takes the log of the copy number AND mu arguments to this function
verbose logical
na.rm The default is to ignore missing values when calculating robust standard deviations

Details

By default, this func estimates the scale parameter for the Normal distribution from the supplied data using the median absolute deviation (MAD). However, different standard deviations can be supplied by the user with the argument sds. The supplied standard deviations must be of the same dimension as the copy number matrix.

Value

array Array of emission probabilities on the log scale. Dimension 1: SNPs, Dimension 2: samples, Dimension3: states

See Also

genotypeEmission, genotypeEmissionCrlmm


[Package VanillaICE version 1.6.0 Index]