VariantAnnotation (version 1.18.5)

GLtoGP: Convert genotype likelihoods to genotype probabilities

Description

Convert an array of genotype likelihoods to posterior genotype probabilities.

Usage

GLtoGP(gl)
PLtoGP(pl)

Arguments

gl

Array of genotype likelihoods (log10-scaled). 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.

pl

Array of genotype likelihoods (phred-scaled, i.e. -10*log10). 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.

Value

An array of posterior genotype probabilities, in the same format as the input (matrix of lists or 3D array).

Details

GLtoGP computes the probability of each genotype as 10^x / sum(10^x). PLtoGP first divides by -10 and then proceeds as in GLtoGP.

See Also

readVcf, genotypeToSnpMatrix

Examples

  ## 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)

  ## Read a vcf file with a "PL" field.
  vcfFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", 
                         package="VariantAnnotation") 
  vcf <- readVcf(vcfFile, "hg19")

  ## extract genotype likelihoods as a matrix of lists
  pl <- geno(vcf)$PL
  class(pl)
  mode(pl)

  # convert to posterior probabilities
  gp <- PLtoGP(pl)