gcount: Calculate genotype counts (additive model) for selected...

In TRD: Transmission Ratio Distortion

Description

Calculate genotype counts (additive model) of case-trios, control-trios and the whole sample, separately for children, mothers and fathers. Additive model means the genotype is the number of copies of minor allele that the individual carries assuming a bi-allelic locus. This genotype will be 0 for homozygous wild-type, 1 for heterozygous, and 2 for homozygous mutant. Minor allele normally refers to the disease allele, which has lower frequency than the alternative allele(s). Trios with partially missing data are included.

Usage

gcount(sample)

Arguments

sample

case- and/or control-trios dataset with first column as disease status (1=case, 0=control), the second, third and forth columns as maternal, paternal and child genotypes. The fifth column, if entered as part of the input data, is the parent-of-origin indicator of disease allele in a heterozygous child (a value of 1 indicates the mother transmitted the disease allele and 0 indicates the father transmitted). The parent-of-origin indicator is only meaningful for a heterozygous child.

Value

cases	genotype counts of children, mothers and fathers, in case-trios
ctrls	genotype counts of children, mothers and fathers, in control-trios
sample	genotype counts of children, mothers and fathers, in the whole sample

Author(s)

Lam Opal Huang

See Also

rtrios

Examples

trios=rtrios(100000,500,0.1,0.2,0.3,1,0.5,0.5,0.1)
gcount(trios$case)
gcount(trios$ctrl)
gcount(rbind(trios$case,trios$ctrl))

TRD documentation built on May 2, 2019, 5:12 a.m.