TRD (version 1.1)

find.maf: Find minor allele frequency (MAF) in case-trios, control-trios, or the whole sample.

Description

Compute MAF in child, parents and triad of case-trios, control-trios, or the whole sample. 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

find.maf(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

MAF in affected children, parents, or triads of case-trios

ctrls

MAF in unaffected children, parents, or triads of control-trios

sample

MAF in children, parents, or triads of the whole sample

See Also

rtrios

Examples

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