Description Usage Arguments Details Value Author(s) References

View source: R/cdfAddPlasqTypes.R

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.

1 | ```
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] 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)

Returns a `list`

structure with the same number of groups as the
`groups`

argument. To each group, one fields is added:

`plasqType` |
A |

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.

affxparser documentation built on Nov. 1, 2018, 2:25 a.m.

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