Knockoffgeneration.enhancer: Knockoff Generation of enhancer

In Iuliana-Ionita-Laza/BIGKnock: BIobank-scale Gene-based association test via Knockoffs

Knockoff Generation of enhancer

Description

This function generates multiple knockoff genotypes for enhancer. The knockoff generations are optimized using shrinkage leveraging algorithm.

Usage

Knockoffgeneration.enhancer(
  G_enhancer_surround = G_enhancer_surround,
  enhancer_start = enhancer_start,
  enhancer_end = enhancer_start,
  M = 5,
  surround.region = 50000,
  LD.filter = 0.75
)

Arguments

G_enhancer_surround	The genotype matrix of the surrounding region for enhancer.
enhancer_start	The start position of enhancer.
enhancer_end	The end position of enhancer.
M	Numer of multiple knockoffs.
surround.region	Surrounding region for enhancer, default is +-50kb.
LD.filter	The correlation threshold for hierarchical clustering. Default LD filter at correlation 0.75

Value

A list file contains original genotype and M knockoff genotypes for enhancer.

Examples

library(Matrix)
data('Knock.generation.enhancer.example')
G_enhancer_surround=Matrix(Knock.generation.enhancer.example$G_enhancer_surround)
pos_enhancer=Knock.generation.enhancer.example$pos_enhancer
enhancer_start=min(pos_enhancer)
enhancer_end=max(pos_enhancer)

G_enhancer_knockoff=Knockoffgeneration.enhancer(G_enhancer_surround=G_enhancer_surround,
                                             enhancer_start=enhancer_start,
                                             enhancer_end=enhancer_end,
                                             M=5,surround.region=50000,LD.filter=0.75)
#M=5 knockoffs
G_enhancer_knockoff1=G_enhancer_knockoff[1,,]
G_enhancer_knockoff2=G_enhancer_knockoff[2,,]
G_enhancer_knockoff3=G_enhancer_knockoff[3,,]
G_enhancer_knockoff4=G_enhancer_knockoff[4,,]
G_enhancer_knockoff5=G_enhancer_knockoff[5,,]

Iuliana-Ionita-Laza/BIGKnock documentation built on July 31, 2023, 3:50 p.m.