| GLtoGP {VariantAnnotation} | R Documentation |
Convert an array of genotype likelihoods to posterior genotype probabilities.
GLtoGP(gl)
gl |
Array of genotype likelihoods. The format can be a matrix of lists, or a three-dimensional array in which the third dimension corresponds to the probabilities for each genotype. |
Computes the probability of each genotype as 10^x / sum(10^x).
An array of posterior genotype probabilities, in the same format as the input (matrix of lists or 3D array).
Stephanie Gogarten <sdmorris@u.washington.edu>
## Read a vcf file with a "GL" field.
vcfFile <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
vcf <- readVcf(vcfFile, "hg19")
## extract genotype likelihoods as a matrix of lists
gl <- geno(vcf)$GL
class(gl)
mode(gl)
# convert to posterior probabilities
gp <- GLtoGP(gl)