mendelErr: Mendelian errors

Description Usage Arguments Details Value Author(s) See Also Examples

Description

Detect Mendelian errors

Usage

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## 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

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

SeqVarTools documentation built on Nov. 22, 2020, 2 a.m.