getCopyNumberScale {VanillaICE} | R Documentation

## Scale parameter used for Gaussian distribution of copy number

### Description

We typically assume that after appropriate transformation the distribution of copy number is approximately Gaussian. This function calculates a robust estimate of the spread based on quantiles of the observed copy number distribution across all autosomes.

### Usage

    getCopyNumberScale(object, ...)

### Arguments

`object` | Object of class `HmmSnpSet` or `HmmSnpCopyNumberSet`
`...` | additional arguments for subsetting the samples

### Details

### Value

A vector of scales with length equal to the number of hidden states (typically 3 or 4)

### Note

### Author(s)

### References

RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136

### See Also

### Examples

[Package VanillaICE version 1.0.2 Index]