GLtoGP {VariantAnnotation} | R Documentation

## 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.

### 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 <sdmorris@u.washington.edu>

### 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)

[Package VariantAnnotation version 1.28.13 Index]