getA {oligo}R Documentation

Compute average log-intensities / log-ratios

Description

Methods to compute average log-intensities and log-ratios across alleles, within strand.

Usage

getA(object)
getM(object)

Arguments

object SnpQSet object.

Details

SNPRMA summarizes the SNP information into 4 quantities (log2-scale):

antisenseThetaA
antisense allele A
antisenseThetaB
antisense allele B
senseThetaA
sense allele A
senseThataB
sense allele B

The average log-intensities are given by: (antisenseThetaA+antisenseThetaB)/2 and (senseThetaA+senseThetaB)/2.

The average log-ratios are given by: antisenseThetaA-antisenseThetaB and senseThetaA-senseThetaB.

Value

A 3-dimensional array (SNP's x Samples x Strand) with the requested measure.
If a Genomewide array (like Affy SNP 6.0) is used, the strand dimension described above is dropped.

See Also

snprma


[Package oligo version 1.6.0 Index]