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affxparser (version 1.44.0)

cdfAddPlasqTypes: Adds the PLASQ types for the probes in a CDF structure

Description

Adds the PLASQ types for the probes in a CDF structure.

This function is design to be used with applyCdfGroups() on an Affymetrix Mapping (SNP) CDF list structure.

Usage

cdfAddPlasqTypes(groups, ...)

Arguments

groups
A list structure with groups. Each group must contain the fields tbase, pbase, and expos.
...
Not used.

Value

Returns a list structure with the same number of groups as the groups argument. To each group, one fields is added:
plasqType
A vector of integers in [0,15].

Details

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 [1], and adds an integer [0,15] interepreted 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, 15=PMcAF.

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)

References

[1] 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.