calculateCnSE {VanillaICE}R Documentation

Calculates copy number standard errors

Description

Calculates SNP-specific standard errors for copy number using a reference set.

Usage

calculateCnSE(object, referenceSet, epsilon = 0.1)

Arguments

object An object of class SnpCopyNumberSet or oligoSnpSet.
referenceSet An object of class SnpCopyNumberSet or oligoSnpSet. If missing, this function uses the samples in the object to estimate across sample standard deviations
epsilon minimum standard error

Details

Calculates SNP-specific standard errors from a reference distribution as the product of the within copy number standard deviation of the sample (test set) and the across samples standard deviation from a reference set. The across samples standard deviation is scaled by the median (e.g., across sample sd = across sample sd/ median(across sample sd)).

Value

A matrix of standard errors

Author(s)

R. Scharpf


[Package VanillaICE version 1.4.0 Index]