mean2g {snpStats} | R Documentation

## Raw coding of posterior probabilities of SNP genotype

### Description

An uncertain SNP genotype call is represented by the three posterior probabilities of the three possible calls. In the class `SnpMatrix`, an approximation to these is packed into a single 1-byte variable of type `raw`. These functions carry out this coding (and decoding).

### Usage

    post2g(p, transpose = FALSE)
    mean2g(m, maxE = FALSE)
    g2post(g, transpose = FALSE)

### Arguments

`p` | A matrix of posterior probabilities. If `transpose` is `FALSE` this is `Nx3`, otherwise `3xN`
`m` | A vector of posterior means
`g` | A `raw` vector of genotype codes
`transpose` | A logical flag indicating transposition of the matric of posterior probabilities (see Description)
`maxE` | A logical flag selecting the maximum entropy option in `mean2g`

### Details

`post2g` and `g2post` convert from posterior probabilities to `raw` code and back respectively. If only the posterior expectation of the genotype (when numerically coded 0, 1, or 2) is available, no unique soultion exists in general and the behaviour of the function is determined by the value of `maxE`. If `TRUE`, then the maximum entropy solutions are returned while, if `FALSE`, an attempt is made to return the least uncertain solution, by setting the posterior probability of the `BB` genotype to zero when the posterior mean is less than 1.0 and the probability of `AA` to zero when the mean is greater than 1.0.

### Value

`post2g` and `mean2g` return a vector of type `raw`. `g2post` returns a numeric matrix.

### Note

These functions are provided mainly for users wishing to write their own data input functions.

### Author(s)

David Clayton dc208@cam.ac.uk

### Examples

    data(testdata)
    g <- Autosomes[1:10, 20] ## A vector of codes
    p <- g2post(g)           ## Transform to probabilities ...
    pg <- post2g(p)          ## ... and back to codes
    m <- p[,2]+2*p[,3]       ## Posterior expectations
    mg <- mean2g(m)          ## Transform to codes ...
    pmg <- g2post(mg)        ## ... and transform to probabilities
    ## Write everything out
    print(cbind(as(g, "numeric"), p, as.numeric(pg), m, as.numeric(mg), pmg))

[Package snpStats version 1.44.0 Index]