Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure.
function is design to be used with
on an Affymetrix Mapping (SNP) CDF
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 .
Note that the above counts can be inferred from the CDF structure alone, i.e. no sequence information is required. Consider a probe group interrogating allele A. First, all PM probes matches the allele A target sequence perfectly regardless of shift. Moreover, all these PM probes mismatch the allele B target sequence at exactly one position. Second, all MM probes mismatches the allele A sequence at exactly one position. This is also true for the allele B sequence, except for an MM probe with zero offset, which only mismatch at one (the middle) position. For a probe group interrogating allele B, the same rules applies with labels A and B swapped. In summary, the mismatch counts for PM probes can take values 0 and 1, and for MM probes they can take values 0, 1, and 2.
list structure with the same number of groups as the
groups argument. To each group, two fields is added:
The number of nucleotides in the probe sequence that mismatches the target sequence of allele A.
The number of nucleotides in the probe sequence that mismatches the target sequence of allele B.
 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.
 Affymetrix, Understanding Genotyping Probe Set Structure, 2005. http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx
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