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.