AlleleSet-methods: Compute average log-intensities / log-ratios

In jmacdon/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

Description

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

Usage

getA(object)
getM(object)
A(object, ...)
B(object, ...)

Arguments

object

SnpQSet, SnpCnvQSet or TilingFeatureSet2 object.

...	arguments to be passed to allele - 'sense' and 'antisense' are valid values if the array is pre-SNP_5.0

Details

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

• antisenseThetaAantisense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

• antisenseThetaBantisense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

• senseThetaAsense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

• senseThataBsense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)

• alleleAAffymetrix 5.0 and 6.0 platforms

• alleleBAffymetrix 5.0 and 6.0 platforms

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

When large data support is enabled with the ff package, the AssayData elements of an AlleleSet object can be ff_matrix or ffdf, in which case pointers to the ff object are stored in the assay data. The functions open and close can be used to open or close the connection, respectively.

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

jmacdon/oligoClasses documentation built on Aug. 11, 2020, 12:32 a.m.