Knockoffgeneration.gene.buffer: Knockoff Generation of Gene buffer region

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

Knockoff Generation of Gene buffer region

Description

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

Usage

Knockoffgeneration.gene.buffer(
  G_gene_buffer_surround = G_gene_buffer_surround,
  gene_buffer_start = gene_buffer_start,
  gene_buffer_end = gene_buffer_end,
  M = 5,
  surround.region = 1e+05,
  LD.filter = 0.75
)

Arguments

G_gene_buffer_surround	The genotype matrix of the surrounding region for gene buffer region.
gene_buffer_start	The start position of gene buffer region.
gene_buffer_end	The end position of gene buffer region.
M	Numer of multiple knockoffs.
surround.region	Surrounding region for gene buffer region, default is +-100kb.
LD.filter	The correlation threshold for hierarchical clustering. Default LD filter at correlation 0.75

Value

G_gene_buffer_knockoff

A list file contains M knockoff genotypes for gene buffer region.

Examples

library(Matrix)
data('Knock.generation.gene.buffer.example')
G_gene_buffer_surround=Matrix(Knock.generation.gene.buffer.example$G_gene_buffer_surround)
pos_gene_buffer=Knock.generation.gene.buffer.example$pos_gene_buffer
gene_buffer_start=min(pos_gene_buffer)
gene_buffer_end=max(pos_gene_buffer)

G_gene_buffer_knockoff=Knockoffgeneration.gene.buffer(G_gene_buffer_surround=G_gene_buffer_surround,
                                               gene_buffer_start=gene_buffer_start,
                                               gene_buffer_end=gene_buffer_end,
                                               M=5,surround.region=100000,LD.filter=0.75)
#M=5 knockoffs
G_gene_buffer_knockoff1=G_gene_buffer_knockoff[1,,]
G_gene_buffer_knockoff2=G_gene_buffer_knockoff[2,,]
G_gene_buffer_knockoff3=G_gene_buffer_knockoff[3,,]
G_gene_buffer_knockoff4=G_gene_buffer_knockoff[4,,]
G_gene_buffer_knockoff5=G_gene_buffer_knockoff[5,,]

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