getHapmapProbabilities {VanillaICE} | R Documentation |
This function is used by the ICE HMM described in the reference below
and currently only supported for 50k and 250k Affymetrix SNP chips. A
nonparametric estimate of the probability that the genotype call is
correct is based on the distribution of crlmm
confidence scores
in the reference HapMap population, where we assume that we know the
true genotype. A similar approach could be used to estimate
probabilities with other genotyping algorithms. See reference below for
more information.
getHapmapProbabilities(object)
object |
One of the HMM classes defined in ICE |
The annotation slot in the object must contain one of the following strings that identifies the Affymetrix chip:
mapping100k (if the 50k xba and 50k hind results have been merged into one object)
pd.mapping50k.xba240 (50k Xba platform)
pd.mapping50k.hind240 (50k Hind)
mapping500k (if the two 250k chips – Nsp and Sty – have been merged)
pd.mapping250k.nsp
pd.mapping250k.sty
A vector of probabilities that the genotype call is correct.
Estimated probabilities are chip-specific. This function is typically not called directly.
RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136