Adds the PLASQ types for the probes in a CDF structure.
function is design to be used with
on an Affymetrix Mapping (SNP) CDF
This function identifies the number of nucleotides (bases) in probe
sequences that mismatch the the target sequence for allele A and the
allele B, as used by PLASQ , and adds an integer [0,15] interpreted
as one of 16 probe types. In PLASQ these probe types are referred to as:
0=MMoBR, 1=MMoBF, 2=MMcBR, 3=MMcBF, 4=MMoAR, 5=MMoAF, 6=MMcAR, 7=MMcAF,
8=PMoBR, 9=PMoBF, 10=PMcBR, 11=PMcBF, 12=PMoAR, 13=PMoAF, 14=PMcAR,
Pseudo rule for finding out the probe-type value:
PM/MM: For MMs add 0, for PMs add 8.
A/B: For Bs add 0, for As add 4.
o/c: For shifted (o) add 0, for centered (c) add 2.
R/F: For antisense (R) add 0, for sense (F) add 1.
Example: (PM,A,c,R) = 8 + 4 + 2 + 0 = 14 (=PMcAR)
list structure with the same number of groups as the
groups argument. To each group, one fields is added:
 LaFramboise T, Weir BA, Zhao X, Beroukhim R, Li C, Harrington D,
Sellers WR, and Meyerson M. Allele-specific amplification in
cancer revealed by SNP array analysis, PLoS Computational Biology,
Nov 2005, Volume 1, Issue 6, e65.
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