gpi {GeneticsPed} | R Documentation

## Genotype probability index

### Description

`gpi` calculates Genotype Probability Index (GPI), which indicates the information content of genotype probabilities derived from segregation analysis.

### Usage

      gpi(gp, hwp)

### Arguments

`gp` | numeric vector or matrix, individual genotype probabilities
`hwp` | numeric vector or matrix, Hard-Weinberg genotype probabilities

### Details

Genotype Probability Index (GPI; Kinghorn, 1997; Percy and Kinghorn, 2005) indicates information that is contained in multi-allele genotype probabilities for diploids derived from segregation analysis, say Thallman et. al (2001a, 2001b). GPI can be used as one of the criteria to help identify which ungenotyped individuals or loci should be genotyped in order to maximise the benefit of genotyping in the population (e.g. Kinghorn, 1999).

`gp` and `hwp` arguments accept genotype probabilities for multi-allele loci. If there are two alleles (1 and 2), you should pass vector of probabilities for genotypes (11 and 12) i.e. one value for heterozygotes (12 and 21) and always skipping last homozygote. With three alleles this vector should hold probabilities for genotypes (11, 12, 13, 22, 23) as also shown bellow and in examples. `hwp` and `gpLong2Wide` functions can be used to ease the setup for `gp` and `hwp` arguments.

         2 alleles: 1 and 2
         11 12
         --> no. dimensions = 2

         3 alleles: 1, 2, and 3
         11 12 13
            22 23
         --> no. dimensions = 5

         ...

         5 alleles: 1, 2, 3, 4, and 5
         11 12 13 14 15
            22 23 24 25
               33 34 35
                  44 45
         --> no. dimensions = 14

In general, number of dimensions (k) for n alleles is equal to:

k = (n * (n + 1) / 2) - 1.

If you have genotype probabilities for more than one individual, you can pass them to `gp` in a matrix form, where each row represents genotype probabilities of an individual. In case of passing matrix to `gp`, `hwp` can still accept a vector of Hardy-Weinberg genotype probabilities, which will be used for all individuals due to recycling. If `hwp` also gets a matrix, then it must be of the same dimension as that one passed to `gp`.

### Value

Vector of N genotype probability indices, where N is number of individuals

### Author(s)

Gregor Gorjanc R code, documentation, wrapping into a package; Andrew Percy and Brian P. Kinghorn Fortran code

### References

Kinghorn, B. P. (1997) An index of information content for genotype probabilities derived from segregation analysis. Genetics 145(2):479-483 http://www.genetics.org/cgi/content/abstract/145/2/479

Kinghorn, B. P. (1999) Use of segregation analysis to reduce genotyping costs. Journal of Animal Breeding and Genetics 116(3):175-180 http://dx.doi.org/10.1046/j.1439-0388.1999.00192.x

Percy, A. and Kinghorn, B. P. (2005) A genotype probability index for multiple alleles and haplotypes. Journal of Animal Breeding and Genetics 122(6):387-392 http://dx.doi.org/10.1111/j.1439-0388.2005.00553.x

Thallman, R. M. and Bennet, G. L. and Keele, J. W. and Kappes, S. M. (2001a) Efficient computation of genotype probabilities for loci with many alleles: I. Allelic peeling. Journal of Animal Science 79(1):26-33 http://jas.fass.org/cgi/reprint/79/1/34

Thallman, R. M. and Bennet, G. L. and Keele, J. W. and Kappes, S. M. (2001b) Efficient computation of genotype probabilities for loci with many alleles: II. Iterative method for large, complex pedigrees. Journal of Animal Science 79(1):34-44 http://jas.fass.org/cgi/reprint/79/1/34

### See Also

`hwp` and `gpLong2Wide`

### Examples

      ## --- Example 1 from Percy and Kinghorn (2005) ---
      ## No. alleles: 2
      ## No. individuals: 1
      ## Individual genotype probabilities:
      ##   Pr(11, 12, 22) = (.1, .5, .4)
      ##
      ## Hardy-Weinberg probabilities:
      ##   Pr(1, 2)   = (.75, .25)
      ##   Pr(11, 12,   (.75^2, 2*.75*.25,
      ##           22) =             .25^2)
      ##               = (.5625, .3750,
      ##                         .0625)

      gp <- c(.1, .5)
      hwp <- c(.5625, .3750)
      gpi(gp=gp, hwp=hwp)

      ## --- Example 1 from Percy and Kinghorn (2005) extended ---
      ## No. alleles: 2
      ## No. individuals: 2
      ## Individual genotype probabilities:
      ##   Pr_1(11, 12, 22) = (.1, .5, .4)
      ##   Pr_2(11, 12, 22) = (.2, .5, .3)

      (gp <- matrix(c(.1, .5, .2, .5), nrow=2, ncol=2, byrow=TRUE))
      gpi(gp=gp, hwp=hwp)

      ## --- Example 2 from Percy and Kinghorn (2005) ---
      ## No. alleles: 3
      ## No. individuals: 1
      ## Individual genotype probabilities:
      ##   Pr(11, 12, 13,   (.1, .5, .0,
      ##          22, 23  =      .4, .0,
      ##              33)            .0)
      ##
      ## Hardy-Weinberg probabilities:
      ##   Pr(1, 2, 3)    = (.75, .25, .0)
      ##   Pr(11, 12, 13,   (.75^2, 2*.75*.25, .0,
      ##          22, 23, =            0.25^2, .0,
      ##              33)                      .0)
      ##                  = (.5625, .3750, .0
      ##                            .0625, .0,
      ##                                   .0)

      gp <- c(.1, .5, .0, .4, .0)
      hwp <- c(.5625, .3750, .0, .0625, .0)
      gpi(gp=gp, hwp=hwp)

      ## --- Example 3 from Percy and Kinghorn (2005) ---
      ## No. alleles: 5
      ## No. individuals: 1
      ## Hardy-Weinberg probabilities:
      ##   Pr(1, 2, 3, 4, 5)   = (.2, .2, .2, .2, .2)
      ##   Pr(11, 12, 13, ...) = (Pr(1)^2, 2*Pr(1)+Pr(2), 2*Pr(1)*Pr(3), ...)
      ##
      ## Individual genotype probabilities:
      ##   Pr(11, 12, 13, ...) = gp / 2
      ##   Pr(12) = Pr(12) + .5

      (hwp <- rep(.2, times=5) %*% t(rep(.2, times=5)))
      hwp <- c(hwp[upper.tri(hwp, diag=TRUE)])
      (hwp <- hwp[1:(length(hwp) - 1)])
      gp <- hwp / 2
      gp[2] <- gp[2] + .5
      gp

      gpi(gp=gp, hwp=hwp)

      ## --- Simulate gp for n alleles and i individuals ---
      n <- 3
      i <- 10

      kAll <- (n*(n+1)/2) # without -1 here!
      k <- kAll - 1
      if(require("gtools")) {
        gp <- rdirichlet(n=i, alpha=rep(x=1, times=kAll))[, 1:k]
        hwp <- as.vector(rdirichlet(n=1, alpha=rep(x=1, times=kAll)))[1:k]
        gpi(gp=gp, hwp=hwp)
      }

[Package GeneticsPed version 1.54.0 Index]