LORSscreen: LORSscreen 'LORSscreen' is a function to solve the...

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

Description

LORSscreen LORSscreen is a function to solve the LORS-Screening optimization problem in Yang et al. (2013)

Usage

LORSscreen(Y, X, lambda, tol)

Arguments

Y	gene expression matrix
X	a SNP
lambda	tuning parameter
tol	a tolerance level

Value

B the estimated coefficients for the SNP

L the estimated hidden factors

mu the estimate for the intercept

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 to build initial estimate

Bhat_initial <- c()
for(SNP_col in 1:ncol(X)){
   X1 <- matrix(X[,SNP_col], ncol = 1)
   LS <- LORSscreen(Y, X1, lambda = 0.1, 0.01)
   B_row <- LS$B
   Bhat_initial <- rbind(Bhat_initial, B_row)
}

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