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]