probabilityToSnpMatrix: Convert posterior genotype probability to a SnpMatrix object
In VariantAnnotation: Annotation of Genetic Variants

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/methods-genotypeToSnpMatrix.R

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

1	probabilityToSnpMatrix(probs)

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.

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

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.

Stephanie Gogarten <sdmorris@u.washington.edu>

genotypeToSnpMatrix, SnpMatrix

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")