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

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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.

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] 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, 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)

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].

Author(s)

Henrik Bengtsson

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.

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.