getA {oligoClasses} | R Documentation |
Methods to compute average log-intensities and log-ratios across alleles, within strand.
getA(object) getM(object)
object |
SnpQSet , SnpCnvQSet or TilingFeatureSet2 object. |
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
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.