mapParams {CNPBayes} | R Documentation

## Parameters for mapping mixture components to distinct copy number states

### Description

Parameters for mapping mixture components to distinct copy number states

### Usage

    mapParams(threshold = 0.1, proportion.subjects = 0.5,
      outlier.variance.ratio = 5, max.homozygous = c(-1.5, -0.5),
      min.foldchange = 1.5)

### Arguments

`threshold` | numeric value in [0, 0.5]. For a given observation (sample), mixture component probabilities > threshold and less than 1-threshold are combined.
`proportion.subjects` | numeric value in [0, 1]. Two components are combined if the fraction of subjects with component probabilities in the range [threshold, 1-threshold] exceeds this value.
`outlier.variance.ratio` | if the ratio of the component variance to the median variance of the other component exceeds the value of this argument, the component is considered to correspond to outliers.
`max.homozygous` | length-2 numeric vector of cutoffs used for establishing a homozygous deletion component. The first element is the cutoff for the mean log R ratios when there are 2 or more states. The second element is the cutoff for the mean log R ratio when there are 3 or more states.
`min.foldchange` | a length-one numeric vector. When there are 3 or more states, we compute the ratio of the distance between the means of the sorted components 1 and 2 (the 2 components with lowest means) and the distance between the means of components 2 and 3. If the ratio (i) exceeds the value specified by this parameter, (ii) there are 3 or more states, and (iii) the first component has a mean less than `max_homozygous[2]`, we infer that the first component is a homozygous deletion.

### Examples

    mapParams()

[Package CNPBayes version 1.13.5 Index]