batchStatisticAccessors {crlmm} | R Documentation

## 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, , ,]

[Package crlmm version 1.38.0 Index]