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]