Example.KnockoffGeneration: Data example for AR Knockoff Generation.

In Iuliana-Ionita-Laza/GeneScan3DKnock: Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes

Data example for AR Knockoff Generation.

Description

This simulated example dataset contains outcome variable Y, covariate X, genotype matrices and genetic variants of surrounding regions for gene buffer and two enhancers separately, positions and functional annotations for gene buffer region, promoter and two enhancers.

Usage

data("KnockoffGeneration.example")

Format

An object of class list of length 17.

Details

We provide genotypes of +-10 Kb neighborhoods for gene buffer region and two enhancers separately. In real data analyses, the neighborhood for knockoff generation should be increase to +-100 Kb.

Examples

data("KnockoffGeneration.example")

Y=KnockoffGeneration.example$Y; X=KnockoffGeneration.example$X; 

G_gene_buffer_surround=KnockoffGeneration.example$G_gene_buffer_surround
variants_gene_buffer_surround=KnockoffGeneration.example$variants_gene_buffer_surround
G_Enhancer1_surround=KnockoffGeneration.example$G_Enhancer1_surround
variants_Enhancer1_surround=KnockoffGeneration.example$variants_Enhancer1_surround
G_Enhancer2_surround=KnockoffGeneration.example$G_Enhancer2_surround
variants_Enhancer2_surround=KnockoffGeneration.example$variants_Enhancer2_surround

gene_buffer.pos=KnockoffGeneration.example$gene_buffer.pos
promoter.pos=KnockoffGeneration.example$promoter.pos
Enhancer1.pos=KnockoffGeneration.example$Enhancer1.pos
Enhancer2.pos=KnockoffGeneration.example$Enhancer2.pos   

Z_gene_buffer=KnockoffGeneration.example$Z_gene_buffer
Z_promoter=KnockoffGeneration.example$Z_promoter
Z_Enhancer1=KnockoffGeneration.example$Z_Enhancer1
Z_Enhancer2=KnockoffGeneration.example$Z_Enhancer2

Iuliana-Ionita-Laza/GeneScan3DKnock documentation built on July 31, 2023, 4:32 a.m.