getA {oligoClasses}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, SnpCnvQSet or TilingFeatureSet2 object.

Details

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

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.

For Tiling data, getM and getA return the log-ratio and average log-intensities computed across channels: M = log2(channel1)-log2(channel2) A = (log2(channel1)+log2(channel2))/2

Value

A 3-dimensional array (SNP's x Samples x Strand) with the requested measure, when the input SNP data (50K, 250K).
A 2-dimensional array (SNP's x Samples), when the input is from SNP 5.0 and SNP 6.0 arrays.
A 2-dimensional array if the input is from Tiling arrays.

See Also

snprma


[Package oligoClasses version 1.6.0 Index]