create_knockoff: Create knockoff genotype data

In KnockoffTrio: GWAS with Trio and Duo Data using Knockoff Statistics for FDR Control

Create knockoff genotype data

Description

Create knockoff genotype data using phased haplotype data.

Usage

create_knockoff(
  trio.hap = NULL,
  duo.hap = NULL,
  pos,
  M = 10,
  maxcor = 0.7,
  maxbp = 80000,
  phasing.dad = NULL,
  phasing.mom = NULL,
  seed = 100
)

Arguments

trio.hap	A 6n*p matrix for trio haplotype data, in which n is the number of trios and p is the number of variants. Each trio must consist of father, mother, and offspring (in this order). The haplotypes must be coded as 0 or 1. Missing haplotypes are not allowed.
duo.hap	A 4m*p matrix for duo haplotype data, in which m is the number of duos and p is the number of variants. Each duo must consist of a single parent and offspring (in this order). The haplotypes must be coded as 0 or 1. Missing haplotypes are not allowed.
pos	A numeric vector of length p for the position of p variants.
M	A positive integer for the number of knockoffs. The default is 10.
maxcor	A real number in a range of [0,1] for hierarchical clustering of neighboring variants used to generate knockoff parents. The default is 0.7.
maxbp	A positive integer for the size of neighboring base pairs used to generate knockoff parents. The default is 80000.
phasing.dad	A numeric vector of length n that contains 1 or 2 to indicate which paternal haplotype was transmitted to offspring in each trio. If NULL, the function will calculate the phasing information based on the input trio haplotype matrix.
phasing.mom	A numeric vector of length n that contains 1 or 2 to indicate which maternal haplotype was transmitted to offspring in each trio. If NULL, the function will calculate the phasing information based on the input trio haplotype matrix.
seed	An integer for the random seed used for knockoff generation.

Value

A list that contains:

trio.ko

A 3n*p*M array for knockoff trio genotype data if trio.hap is provided.

duo.ko

A 3m*p*M array for knockoff duo genotype data if duo.hap is provided.

duo

A 3m*p matrix for duo genotype data if duo.hap is provided.

Examples

data(KnockoffTrio.example)
knockoff<-create_knockoff(trio.hap=KnockoffTrio.example$trio.hap,
          duo.hap=KnockoffTrio.example$duo.hap, pos=KnockoffTrio.example$pos, M=10)

KnockoffTrio documentation built on April 4, 2025, 2:14 a.m.