HC_Screening: HC_Screening 'HC_Screening' is a function to apply the...

In jdrhyne2/FastLORS: Joint Modeling for eQTL Mapping in R

Description

HC_Screening HC_Screening is a function to apply the HC-Screening screening method of Rhyne et al. (2018) (In progress) Note: HC-Screening ranks SNPs by their higher criticism statistics and selects the top n, where n is the number of samples

Usage

HC_Screening(Y, X)

Arguments

Y	gene expression matrix
X	matrix of SNPs

Value

selectedSNPs The SNPs selected by HC-Screening

Examples

## Example

## Generate some data
n <- 50
p <- 200
q <- 100
k <- 10
set.seed(123)
X <- matrix(rbinom(n*p,1,0.5),n,p)
L <- matrix(rnorm(n*k),n,k) %*% t(matrix(rnorm(q*k),q,k))
B <- matrix(0, ncol(X), ncol(L))
activeSNPs <- sort(sample(c(1:nrow(B)), 20))
for(i in 1:length(activeSNPs)){
genes_influenced <- sort(sample(c(1:ncol(B)),5))
B[activeSNPs[i], genes_influenced] <- 2
}
E <- matrix(rnorm(n*q),n,q)
Y <- X %*% B + L + E

## Usage
HC_Screening(Y, X)

jdrhyne2/FastLORS documentation built on March 5, 2020, 6:50 a.m.