genotypeEmissionCrlmm {VanillaICE} | R Documentation |
Estimate the emission probabilities that incorporate information on the confidence scores for the genotype calls.
genotypeEmissionCrlmm(genotypes, conf, pHetCalledHom = 0.001, pHetCalledHet = 0.995, pHomInNormal = 0.99, pHomInRoh = 0.999, annotation)
genotypes |
Matrix of genotypes |
conf |
Matirx of confidence scores (see details). |
pHetCalledHom |
The probability that a truly heterozygous SNP is incorrectly called homozygous (incorrect call). |
pHetCalledHet |
The probability that a truly heterozygous SNP is called heterozygous (correct call). |
pHomInNormal |
The probability of a homozygous genotype call in the 'normal' state. |
pHomInRoh |
The probability of a homozygous genotype call in a region of homozygosity. |
annotation |
The cdf name (e.g., "genomewidesnp6") |
The confidence scores by crlmm are saved as an integer: 1000*log(1-p), where p is the probability that the genotype call is correct.
The reference distribution of confidence scores are available for the following Affymetrix platforms: affy6, nsp250, and sty250k.
An R x C x X array of emission probabilities, where
R = number of loci (SNPs)
C = number of samples
S = number of states
R Scharpf
RB Scharpf et al. (2008), Annals of Applied Statistics