Description Usage Arguments Details Value See Also
Methods to compute average logintensities and logratios across alleles, within strand.
1 2 3 4 
object 

... 
arguments to be passed to 
For SNP data, SNPRMA summarizes the SNP information into 4 quantities (log2scale):
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 logintensities are given by:
(antisenseThetaA+antisenseThetaB)/2
and
(senseThetaA+senseThetaB)/2
.
The average logratios are given by:
antisenseThetaAantisenseThetaB
and
senseThetaAsenseThetaB
.
For Tiling data, getM
and getA
return the logratio and
average logintensities 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.
A 3dimensional array (SNP's x Samples x Strand) with the requested measure, when the input SNP data (50K, 250K).
A 2dimensional array (SNP's x Samples), when the input is from SNP 5.0 and SNP 6.0 arrays.
A 2dimensional array if the input is from Tiling arrays.
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