cdfAddBaseMmCounts: Adds the number of allele A and allele B mismatching...

Description Usage Arguments Details Value Author(s) References See Also

View source: R/cdfAddBaseMmCounts.R

Description

Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure.

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

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 [1].

Usage

1

Arguments

groups

A list structure with groups. Each group must contain the fields tbase, pbase, and offset (from cdfAddProbeOffsets()).

...

Not used.

Details

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.

Value

Returns a list structure with the same number of groups as the groups argument. To each group, two fields is added:

mmACount

The number of nucleotides in the probe sequence that mismatches the target sequence of allele A.

mmBCount

The number of nucleotides in the probe sequence that mismatches the target sequence of allele B.

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.
[2] Affymetrix, Understanding Genotyping Probe Set Structure, 2005. http://www.affymetrix.com/support/developer/whitepapers/genotyping_probe_set_structure.affx

See Also

To add required probe offsets, cdfAddProbeOffsets(). applyCdfGroups().


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