probabilityToSnpMatrix {VariantAnnotation} | R Documentation |
Convert a matrix of posterior genotype probabilites P(AA), P(AB), P(BB) to a SnpMatrix.
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")