R: Adds the number of allele A and allele B mismatching...
cdfAddBaseMmCounts
R Documentation
Adds the number of allele A and allele B mismatching nucleotides of the probes in a CDF structure
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
cdfAddBaseMmCounts(groups, ...)
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().