INFRA: Exact tests

Conduct exact tests against AlphaSimR, simplePHENOTYPES and the simulation framework described in ARG-Needle paper.

data/simulate_AlphaSimR.R

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+if (!require("AlphaSimR")) install.packages("AlphaSimR", repos='http://cran.us.r-project.org')
+library(AlphaSimR)
+if (!require("reticulate")) install.packages("reticulate", repos='http://cran.us.r-project.org')
+library(reticulate)
+if (!require("tidyr")) install.packages("tidyr", repos='http://cran.us.r-project.org')
+
+# This code is used from verification.py to simulate quantitative traits
+# by using AlphaSimR.
+#
+# The basic simulation step is the following:
+# 1. Use the tskit Python package through the R package tskit and load the tree
+#   sequence data as a founder population in AlphaSimR. The codes of this step are
+#   largely adapted from
+#   https://github.com/ ynorr/AlphaSimR_Examples/blob/master/misc/msprime.R
+# 2. Simulate quantitative traits of the founder population in AlphaSimR
+
+# The commandline input has 8 elements
+# [num_causal, temporary_directory_name, tree_filename, phenotype_filename,
+# trait_filename, corA, num_trait, random_seed]
+myArgs <- commandArgs(trailingOnly = TRUE)
+# Convert to numerics
+num_causal <- as.numeric(myArgs[1])
+directory_name <- myArgs[2]
+tree_filename <- myArgs[3]
+phenotype_filename <- myArgs[4]
+trait_filename <- myArgs[5]
+corA <- as.numeric(myArgs[6])
+num_trait <- as.numeric(myArgs[7])
+random_seed <- as.numeric(myArgs[8])
+
+set.seed(random_seed)
+
+tskit <- import("tskit")
+
+tree_filename <- paste0(directory_name,"/", tree_filename,".tree")
+ts <- tskit$load(tree_filename)
+
+sites <- ts$tables$sites$asdict()
+pos <- sites$position * 1e-8 # Convert to Morgans
+pos <- pos - pos[1] # Set first position to zero
+
+# Extract haplotypes
+haplo <- t(ts$genotype_matrix())
+
+# Create an AlphaSimR founder population
+founderPop <- newMapPop(genMap=list(pos), haplotypes=list(haplo))
+
+num_ind <- nrow(haplo) / 2
+
+if (num_trait == 1){
+  mean <- 0
+  var <- 1
+  corA <- NULL
+  H2 <- 1
+} else if (num_trait == 2){
+  mean <- c(0,0)
+  var <- c(1,1)
+  corA <- matrix(c(1,corA,corA,1),nrow=2,ncol=2)
+  H2 <- c(1,1)
+}
+
+SP <- SimParam$
+  new(founderPop)$
+  addTraitA(
+    nQtlPerChr=num_causal,
+    mean=mean,
+    var=var,
+    corA=corA
+  )$
+  setVarE(H2=H2)
+
+individuals <- newPop(founderPop)
+
+trait_df <- c()
+phenotype_df <- c()
+
+for (trait_id in 1:num_trait){
+  qtl_site <- SP$traits[[trait_id]]@lociLoc - 1
+  effect_size <- SP$traits[[trait_id]]@addEff
+  trait_id_df <- data.frame(
+    effect_size = effect_size,
+    site_id = qtl_site,
+    trait_id = rep(trait_id-1, length(effect_size))
+  )
+  trait_df <- rbind(trait_df, trait_id_df)
+  phenotype <- individuals@pheno[,trait_id]
+  phenotype_id_df <- data.frame(
+    phenotype=phenotype,
+    individual_id = 0:(num_ind-1),
+    trait_id = rep(trait_id-1, num_ind)
+  )
+  phenotype_df <- rbind(phenotype_df, phenotype_id_df)
+}
+
+phenotype_filename <- paste0(directory_name,"/",phenotype_filename,".csv")
+write.csv(phenotype_df, phenotype_filename, row.names=FALSE)
+
+trait_filename <- paste0(directory_name,"/",trait_filename,".csv")
+write.csv(trait_df, trait_filename, row.names=FALSE)

data/simulate_simplePHENOTYPES.R

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+if (!require("simplePHENOTYPES")) install.packages("simplePHENOTYPES", repos='http://cran.us.r-project.org')
+library(simplePHENOTYPES)
+if (!require("reticulate")) install.packages("reticulate", repos='http://cran.us.r-project.org')
+library(reticulate)
+
+# This code is used from verification.py to simulate quantitative traits
+# by using simplePHENOTYPES.
+
+# This code loads the vcf file and simulates quantitative traits
+
+# The commandline input has 7 elements
+# [num_causal, num_trait, add_effect, add_effect_2, directory_name,
+# vcf_filename, random_seed]
+myArgs <- commandArgs(trailingOnly = TRUE)
+
+num_causal <- as.numeric(myArgs[1])
+num_trait <- as.numeric(myArgs[2])
+add_effect <- as.numeric(myArgs[3])
+add_effect_2 <- as.numeric(myArgs[4])
+directory_name <- myArgs[5]
+vcf_filename <- myArgs[6]
+random_seed <- as.numeric(myArgs[7])
+
+if (num_trait == 1){
+  effect <- add_effect
+  mean <- 0
+  h2 <- 1
+} else if (num_trait == 2){
+  effect <- c(add_effect, add_effect_2)
+  mean <- c(0,0)
+  h2 <- c(1,1)
+}
+
+suppressMessages(create_phenotypes(
+  geno_file = paste0(directory_name, "/", vcf_filename, ".vcf"),
+  add_QTN_num = num_causal,
+  add_effect = effect,
+  rep = 1,
+  h2 = h2,
+  model = "A",
+  seed = random_seed,
+  vary_QTN = FALSE,
+  to_r = FALSE,
+  sim_method = "geometric",
+  quiet = TRUE,
+  home_dir = directory_name,
+  verbose = FALSE,
+  mean = mean,
+  ntraits = num_trait
+))