VariantAnnotation (version 1.18.5)

probabilityToSnpMatrix: Convert posterior genotype probability to a SnpMatrix object

Description

Convert a matrix of posterior genotype probabilites P(AA), P(AB), P(BB) to a SnpMatrix.

Usage

probabilityToSnpMatrix(probs)

Arguments

probs

Matrix with three columns for the posterior probabilities of the three genotypes: "P(A/A)", "P(A/B)", "P(B/B)". Each row must sum to 1.

Value

An object of class "SnpMatrix" with one row (one sample). Posterior probabilities are encoded (approximately) as byte values, one per SNP. See the help page for SnpMatrix for complete details of the class structure.

Details

probabilityToSnpMatrix converts a matrix of posterior probabilites of genotype calls into a SnpMatrix.

See Also

genotypeToSnpMatrix, SnpMatrix

Examples

probs <- matrix(c(1,0,0,
                  0,1,0,
                  0,0,1,
                  NA,NA,NA),
                  ncol=3, byrow=TRUE,
                  dimnames=list(1:4,c("A/A","A/B","B/B")))
sm <- probabilityToSnpMatrix(probs)
as(sm, "character")