mendelErr: Mendelian errors

Description

Detect Mendelian errors

Usage

"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.

Value

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.

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.

Examples

Run this code

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