R: function to set impossible genotypes as missing

Xfix {GenABEL} | R Documentation

## function to set impossible genotypes as missing

### Description

Sets impossible genotypes (e.g. heterozygous male X-linked genotypes) to missing

### Usage

    	Xfix(data)

### Arguments

`data` | Object of gwaa.data-class

### Details

Sets to missing genotypes in the following situations: (1) heterozygous male X-genotypes (2) heterozygous Y- and mtDNA genotypes (3) any Y-genotypes in females. Should only be used after `check.marker`, which identifies systematic sex errors.

### Value

The same object of gwaa.data-class, with fixed genotypes

### Author(s)

Yurii Aulchenko

### See Also

`check.marker`

### Examples

    require(GenABEL.data)
    data(ge03d2c)
    # truncate the data to make the example faster
    ge03d2c <- ge03d2c[seq(from=1,to=nids(ge03d2c),by=2),seq(from=1,to=nsnps(ge03d2c),by=2)]
    # many errors
    mc0 <- check.marker(ge03d2c)
    # take only people and markers passing QC
    fixed0 <- ge03d2c[mc0$idok,mc0$snpok]
    # major errors fixed, still few males are heterozygous for X-chromsome markers
    mc1 <- check.marker(fixed0)
    # fix minor X-chromosome problems
    fixed1 <- Xfix(fixed0)
    # no errors
    mc2 <- check.marker(fixed1)
    summary(mc2)

[Package GenABEL version 1.8-0 Index]