Methods to compute average log-intensities and log-ratios across alleles, within strand.
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arguments to be passed to
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:
The average log-ratios are given by:
For Tiling data,
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
ffdf, in which case pointers to the ff
object are stored in the assay data. The functions
close can be used to open or close the connection,
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.
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