misinherits {snpStats} | R Documentation

## Find non-Mendelian inheritances in family data

### Description

For SNP data in families, this function locates all subjects whose parents are in the dataset and tests each SNP for non-Mendelian inheritances in these trios.

### Usage

    misinherits(ped, id, father, mother, data = sys.parent(), snp.data)

### Arguments

`ped` | Pedigree identifiers
`id` | Subject identifiers
`father` | Identifiers for subjects' fathers
`mother` | Identifiers for subjects' mothers
`data` | A data frame in which to evaluate the previous four arguments
`snp.data` | An object of class `"SnpMatrix"` containing the SNP genotypes to be tested

### Details

The first four arguments are usually derived from a "pedfile". If a data frame is supplied for the `data` argument, the first four arguments will be evaluated in this frame. Otherwise they will be evaluated in the calling environment. If the arguments are missing, they will be assumed to be in their usual positions in the pedfile data frame i.e. in columns one to four. If the pedfile data are obtained from a dataframe, the row names of the `data` and `snp.data` files will be used to align the pedfile and SNP data. Otherwise, these vectors will be assumed to be in the same order as the rows of `snp.data`.

### Value

A logical matrix. Rows are subjects with any non-Mendelian inheritances and columns are SNPs with any non-Mendelian inheritances. The body of the matrix details whether each subject has non-Mendelian inheritance at each SNP. If a subject has no recorded genotype for a specific SNP, the corresponding element of the output matrix is set to NA.

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`tdt.snp`

### Examples

    data(families)
    misinherits(data=pedData, snp.data=genotypes)

[Package snpStats version 1.40.0 Index]