mendelErr: Mendelian errors

In smgogarten/SeqVarTools: Tools for variant data

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)

smgogarten/SeqVarTools documentation built on July 4, 2023, 2:34 a.m.