batchStatisticAccessors: Accessors for batch-specific summary statistics.

In benilton/crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Accessors for batch-specific summary statistics.

Description

The summary statistics stored here are used by the tools for copy number estimation.

Usage

corr(object, ...)
tau2(object, ...)
mads(object,...)
medians(object,...)
Ns(object,...)

Arguments

object	An object of class CNSet.
...	Ignored

Value

An array with dimension R x A x G x C, or R x G x C.

R: number of markers A: number of alleles (2) G: number of biallelic genotypes (3) C: number of batches

Ns returns an array of genotype frequencies stratified by batch. Dimension R x G x C.

corr returns an array of within-genotype correlations (log2-scale) stratified by batch. Dimension R x G x C.

medians returns an array of the within-genotype medians (intensity-scale) stratified by batch and allele. Dimension R x A x G x C.

mads returns an array of the within-genotype median absolute deviations (intensity-scale) stratified by batch and allele. Dimension is the same as for medians.

tau2 returns an array of the squared within-genotype median absolute deviation on the log-scale. Only the mads for AA and BB genotypes are stored. Dimension is R x A x G x C, where G is AA or BB. Note that the mad for allele A/B for subjects with genotype BB/AA is a robust estimate of the background variance, whereas the the mad for allele A/B for subjects with genotype AA/BB is a robust estimate of the variance for copy number greater than 0 (we assume that on the log-scale the variance is rougly constant for CA, CB > 0).

See Also

batchStatistics

Examples

data(cnSetExample)
Ns(cnSetExample)[1:5, , ]
corr(cnSetExample)[1:5, , ]
meds <- medians(cnSetExample)
mads(cnSetExample)[1:5, , ,]
tau2(cnSetExample)[1:5, , ,]

benilton/crlmm documentation built on June 10, 2025, 8:13 p.m.