oligo (version 1.36.1)

getA: 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)
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

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.

code

close

Details

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

• antisenseThetaA

{antisense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)} antisenseThetaB{antisense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)} senseThetaA{sense allele A. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)} senseThataB{sense allele B. (Not applicable for Affymetrix 5.0 and 6.0 platforms.)} alleleA{Affymetrix 5.0 and 6.0 platforms} alleleB{Affymetrix 5.0 and 6.0 platforms}

See Also

snprma