Accessors for batch-specific summary statistics.

Description

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

Usage

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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

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