R: Fill holes in genotype data

fill.geno {qtl} | R Documentation

## Fill holes in genotype data

### Description

Replace the genotype data for a cross with a version imputed either by simulation with `sim.geno`, by the Viterbi algorithm with `argmax.geno`, or simply filling in genotypes between markers that have matching genotypes.

### Usage

    fill.geno(cross, method=c("imp","argmax", "no_dbl_XO", "maxmarginal"),
              error.prob=0.0001,
              map.function=c("haldane","kosambi","c-f","morgan"),
              min.prob=0.95)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`method` | Indicates whether to impute using a single simulation replicate from `sim.geno`, using the Viterbi algorithm, as implemented in `argmax.geno`, by simply filling in missing genotypes between markers with matching genotypes, or by choosing (at each marker) the genotype with maximal marginal probability.
`error.prob` | Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype).
`map.function` | Indicates whether to use the Haldane, Kosambi or Carter-Falconer map function when converting genetic distances into recombination fractions.
`min.prob` | For `method="maxmarginal"`, genotypes with probability greater than this value will be imputed; those less than this value will be made missing.

### Details

This function is written so that one may perform rough genome scans by marker regression without having to drop individuals with missing genotype data. We must caution the user that little trust should be placed in the results.

With `method="imp"`, a single random imputation is performed, using `sim.geno`.

With `method="argmax"`, for each individual the most probable sequence of genotypes, given the observed data (via `argmax.geno`), is used.

With `method="no_dbl_XO"`, non-recombinant intervals are filled in; recombinant intervals are left missing. For example, a sequence of genotypes like `A---A---H---H---A` (with `A` and `H` corresponding to genotypes AA and AB, respectively, and with `-` being a missing value) will be filled in as `AAAAA---HHHHH---A`.

With `method="maxmarginal"`, the conditional genotype probabilities are calculated with `calc.genoprob`, and then at each marker, the most probable genotype is determined. This is taken as the imputed genotype if it has probability greater than `min.prob`; otherwise it is made missing.

With `method="no_dbl_XO"` and `method="maxmarginal"`, some missing genotypes likely remain. With `method="maxmarginal"`, some observed genotypes may be made missing.

### Value

The input `cross` object with the genotype data replaced by an imputed version. Any intermediate calculations (such as is produced by `calc.genoprob`, `argmax.geno` and `sim.geno`) are removed.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`sim.geno`, `argmax.geno`

### Examples

    data(hyper)

    out.mr <- scantwo(fill.geno(hyper,method="argmax"), method="mr")
    plot(out.mr)

[Package qtl version 1.41-6 Index]