cdfAddPlasqTypes {affxparser} | R Documentation |
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.
cdfAddPlasqTypes(groups, ...)
groups |
A |
... |
Not used. |
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)
Returns a list
structure with the same number of groups as the
groups
argument. To each group, one fields is added:
plasqType |
Henrik Bengtsson
[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.