getCallEmission {VanillaICE}R Documentation

Calculates emission probabilities for genotype calls

Description

Calculates emission probabilities for genotype calls. Only used by the ICE HMM.

Usage


getCallEmission(object, CALL.STATES = 2, SAMPLE = 1, P.HOM.CHOM = 0.999,
P.HET.CHOM = 1 - 0.999, P.HET.CHET = 0.999, P.HOM.CHET = 1 - 0.999,
P.CHOM.Normal, P.CHOM.LOH, hapmapP)

Arguments

object Typically an object of class HmmSnpCallSet
CALL.STATES Integer: number of hidden states (default is 2 – loss of heterozygosity and retention of heterozygosity)
SAMPLE Integer: which sample to extract genotype calls from the HmmSnpCallSet object
P.HOM.CHOM Numeric. Probability that the true genotype is homozygous (AA or BB) given that the observed genotype was homozygous (AA or BB)
P.HET.CHOM Numeric. Probability that the true genotype is heterozygous (AB) given that the observed genotype was homozygous.
P.HET.CHET Numeric. Probability that the true genotype is heterozygous (AB) given that the observed genotype was heterozygous.
P.HOM.CHET Numeric. Probability that the true genotype is homozygous given that the observed genotype was heterozygous.
P.CHOM.Normal Numeric. Probability that the observed genotype is homozygous if the true hidden state is retention of heterozygosity.
P.CHOM.LOH Numeric. Probability that the observed genotype is homozygous given that the true hidden state is loss of heterozygosity.
hapmapP A matrix estimated from 269 HapMap samples. See details.

Details

We group the CRLMM probabilities of a correct genotype call for the 269 HapMap samples into 1 of 4 possible categories:

1: genotype call is HET, truth is HOM 2: genotype call is HET, truth is HET 3: genotype call is HOM, truth is HOM 4: genotype call is HOM, truth is HET

Value

Returns matrix of emission probabilities that are a function of the confidence scores provided by crlmm for genotype calls.

Note

Not typically called directly.

Author(s)

References

RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136

See Also

The R package callsConfidence: http://www.biostat.jhsph.edu/~rscharpf/software/index.html

callEmission, hmm, crlmm

Examples






[Package VanillaICE version 1.0.2 Index]