Example.GeneScan3D: Data example for GeneScan3D (gene-based testing by...

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

Data example for GeneScan3D (gene-based testing by integrating long-range chromatin interactions).

Description

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

Usage

data("GeneScan3D.example")

Format

An object of class list of length 12.

Details

We generated genotypes for 2,000 individuals in a 14.5 Kb gene region, a promoter as a 0.5 Kb segment upstream of the TSS (the start point of the gene) and R = 2 enhancers with length 2 KB, which are outside the 15 Kb gene plus promoter region.

Examples

data("GeneScan3D.example")

Y=GeneScan3D.example$Y; X=GeneScan3D.example$X; n=length(Y)

G_gene_buffer=GeneScan3D.example$G_gene_buffer
G_promoter=GeneScan3D.example$G_promoter
G_EnhancerAll=cbind(GeneScan3D.example$G_Enhancer1,GeneScan3D.example$G_Enhancer2)

Z_gene_buffer=GeneScan3D.example$Z_gene_buffer
Z_promoter=GeneScan3D.example$Z_promoter
Z_EnhancerAll=rbind(GeneScan3D.example$Z_Enhancer1,GeneScan3D.example$Z_Enhancer2)

pos_gene_buffer=GeneScan3D.example$pos_gene_buffer

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