mendelErr {SeqVarTools} | R Documentation

## Mendelian errors

### Description

Detect Mendelian errors

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    mendelErr(gdsobj, pedigree, use.names=FALSE,
    autosomes=1:22, xchrom="X", ychrom="Y", verbose=TRUE)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`pedigree` | A data.frame with columns (family, individ, father, mother, sex, sample.id). "sex" column should have values "M"/"F". "sample.id" values should correspond to "sample.id" in `gdsobj`.
`use.names` | A logical indicating whether to assign variant IDs as names of the output vector.
`autosomes` | A vector with chromosome values in `gdsobj` corresponding to autosomes.
`xchrom` | The chromosome value in `gdsobj` corresponding to the X chromosome.
`ychrom` | The chromosome value in `gdsobj` corresponding to the Y chromosome.
`verbose` | A logical indicating whether to print the number of samples selected for each trio.

### Details

Mendelian errors are detected for each trio in `pedigree`. Duos (mother or father missing) are included. The pedigree must have only one sample per individual.

### Value

A list with the following elements:

`by.variant` | An integer vector with the number of mendelian errors detected for each variant. If `use.names=TRUE`, the vector will be named with variant IDs.
`by.trio` | An integer vector with the number of mendelian errors detected for each trio. The vector will be named with the sample ID of the child in each trio.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    data(pedigree)
    err <- mendelErr(gds, pedigree)
    table(err$by.variant)
    err$by.trio
    seqClose(gds)

[Package SeqVarTools version 1.26.0 Index]