Adding artificial gwas generation

Code/Data/gen_gwas.R

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+# npdro::createSimulation2() example for gwas simulation
+if (!require("devtools")) install.packages("devtools")
+library(devtools)
+install_github("insilico/npdro")  
+library(npdro)
+
+## Set Working Directory to file directory - RStudio approach
+setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
+
+gen.gwas = function(samples, vars, batch_size=1000){
+  for (x in 1:ceiling(samples/batch_size)){
+      curr_batch <- samples - (batch_size*(x-1))
+      batch_gen <- ifelse(curr_batch > batch_size, batch_size, curr_batch)
+      data <- createSimulation2(data.type = "discrete", avg.maf = 0.2, 
+                    sim.type = "mainEffect",
+                    pct.train = 1.0, 
+                    pct.imbalance=round(runif(n = 1, min = 0.1, max = 0.9),2), 
+                    main.bias = 0.4, pct.signals = 0.2,
+                    num.samples = batch_gen,
+                    num.variables = vars)
+      
+        rownames(data$train) <- as.integer(rownames(data$train))+
+          (batch_size*(x-1))
+      
+      if (x == 1){
+        write.table(data$train, "artif_gwas.csv", row.names = TRUE)
+      } else{
+          write.table(data$train, "artif_gwas.csv", row.names = TRUE, 
+                    append = TRUE, col.names = FALSE)
+      }
+  }
+  return(data$train)
+}
+
+gen.gwas(1000000, 10000)
+

Code/Schrick-Noah_CS-6643_Research-Project.cpp

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+#include <boost/mpi.hpp>
+#include <boost/mpi/environment.hpp>
+
+#include <plinkio/plinkio.h>
+#include <Rcpp.h>

Code/Schrick-Noah_CS-6643_Research-Project.h

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+

Presentations/.~lock.Schrick-Noah_CS-6643_Proposal.ppt#

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+,noah,NovaArchSys,03.12.2022 18:36,file:///home/noah/.config/libreoffice/4;