GhostKnockoff.prelim {GhostKnockoff}

Preliminary data management for GhostKnockoff

Description

This function does the preliminary data management and pre-computes matrices for GhostKnockoff inference, given pre-computed correlation matrix of the variants (e.g. using reference panel in genetic studies). The output will be passed to the other functions.

Usage

GhostKnockoff.prelim(cor.G,M=5,method='asdp',max.size=500)

Arguments

cor.G

The pre-computed correlation matrix of the variants.

M

Hypothetical number of knockoffs per variant. The default is 5 for multiple knockoff inference.

method

Either "sdp" or "asdp" (default: "asdp"). This determines the method that will be used to minimize the correlation between the original variables and the knockoffs.

max.size

The maximum number in each cluster in the "asdp" method. The default is 500. It will be ignored for "sdp".

Value

It returns a list that will be passed to function GhostKnockoff.fit().

Examples

# We use genetic data as an example
library(GhostKnockoff)

# load example vcf file from package "seqminer", this serves as the reference panel
vcf.filename = system.file("vcf/1000g.phase1.20110521.CFH.var.anno.vcf.gz", package = "seqminer")

## this is how the actual genotype matrix from package "seqminer" looks like
example.G <- t(readVCFToMatrixByRange(vcf.filename, "1:196621007-196716634",annoType='')[[1]])
example.G <- example.G[,apply(example.G,2,sd)!=0]
example.G <- example.G[,1:100]

# compute correlation among variants
cor.G<-matrix(as.numeric(corpcor::cor.shrink(example.G)), nrow=ncol(example.G))

# fit null model
GhostKnockoff.prelim(cor.G,M=5,method='asdp',max.size=500)