GLtoGP: Convert genotype likelihoods to genotype probabilities

In Jiefei-Wang/VariantAnnotation: Annotation of Genetic Variants

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.

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.

Value

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

Author(s)

Stephanie Gogarten <[e-mail]>

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)

Jiefei-Wang/VariantAnnotation documentation built on March 19, 2020, 12:03 a.m.