Test using different Regulator or Targets in GENIE3, do I get the same output. It depends. Regulator-No; Target-Yes.

GENIE3_quick_test.R

# Test on GENIE3 whether
# (Q1) if using more genes as regulator, for the same regulator-target edge 
# do I get the same order? No. The edge order will be different.

# (Q2) if using more genes as targets, for the same regulator-target edges,
# do I get the same order? Yes. The same edge will have the exact same weight.

# Author: Ji Huang
# Date: 2021-01-06


# 0. Prep -----------------------------------------------------------------

library(GENIE3)
library(tidyverse)

exprMatr <- matrix(sample(1:10, 1000, replace=TRUE), 
                   ncol=20)

rownames(exprMatr) <- paste("Gene", 1:nrow(exprMatr), sep="")
colnames(exprMatr) <- paste("Sample", 1:ncol(exprMatr), sep="")
head(exprMatr)


# 1. Answer Q1 ------------------------------------------------------------

regulators <- c(1:10)
set.seed(123)
weightMat <- GENIE3(exprMatr, regulators=regulators)
linkList1 <- getLinkList(weightMat)
#head(linkList1)
head(linkList1 %>% filter(regulatoryGene == "Gene4"))

regulators <- c(1:20)
set.seed(123)
weightMat <- GENIE3(exprMatr, regulators=regulators)
linkList2 <- getLinkList(weightMat)

linkList2_filter <- linkList2 %>% 
    filter(regulatoryGene  %in% linkList1$regulatoryGene )

head(linkList2_filter %>% filter(regulatoryGene == "Gene4"))



# 2. Answer Q2 ------------------------------------------------------------

regulators <- c(1:10)
targets <- c(1:20)
set.seed(123)
weightMat <- GENIE3(exprMatr, regulators=regulators,
                    targets = targets)
linkList1 <- getLinkList(weightMat)
head(linkList1)


regulators <- c(1:10)
targets <- c(1:30)
set.seed(123)
weightMat <- GENIE3(exprMatr, regulators=regulators,
                    targets = targets)
linkList2 <- getLinkList(weightMat)

linkList2_filter <- linkList2 %>% 
    filter(targetGene %in% linkList1$targetGene)
head(linkList2_filter)