probabilityToSnpMatrix {VariantAnnotation} | R Documentation

## 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.

### Details

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

### 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.

### Author(s)

Stephanie Gogarten <sdmorris@u.washington.edu>

### 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")

[Package VariantAnnotation version 1.30.1 Index]