Convert genotype likelihoods to genotype probabilities

Description

Convert an array of genotype likelihoods to posterior genotype probabilities.

Usage

GLtoGP(gl)
PLtoGP(pl)

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(VariantAnnotation)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/VariantAnnotation/GLtoGP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GLtoGP
> ### Title: Convert genotype likelihoods to genotype probabilities
> ### Aliases: GLtoGP PLtoGP
> ### Keywords: manip
> 
> ### ** 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)$GL
>   class(gl)
[1] "matrix"
>   mode(gl)
[1] "list"
> 
>   # convert to posterior probabilities
>   gp <- GLtoGP(gl)
> 
>   ## Read a vcf file with a "PL" field.
>   vcfFile <- system.file("extdata", "hapmap_exome_chr22.vcf.gz", 
+                          package="VariantAnnotation") 
>   vcf <- readVcf(vcfFile, "hg19")
Warning message:
In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
> 
>   ## extract genotype likelihoods as a matrix of lists
>   pl <- geno(vcf)$PL
>   class(pl)
[1] "matrix"
>   mode(pl)
[1] "list"
> 
>   # convert to posterior probabilities
>   gp <- PLtoGP(pl)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>