getCallEmission {VanillaICE} | R Documentation |
Calculates emission probabilities for genotype calls. Only used by the ICE HMM.
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)
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. |
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
Returns matrix of emission probabilities that are a function of the
confidence scores provided by crlmm
for genotype calls.
Not typically called directly.
RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136
The R package callsConfidence: http://www.biostat.jhsph.edu/~rscharpf/software/index.html