misinherits: Find non-Mendelian inheritances in family data

In snpStats: SnpMatrix and XSnpMatrix classes and methods

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 [e-mail]

See Also

tdt.snp

Examples

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

snpStats documentation built on Nov. 8, 2020, 10:59 p.m.