--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MatrixEQTL/demo/q.qqplot.r	Fri Mar 12 08:20:57 2021 +0000
@@ -0,0 +1,43 @@
+library("MatrixEQTL")
+
+# Number of samples
+n = 100;
+
+# Number of variables
+ngs = 2000;
+
+# Common signal in all variables (population stratification)
+pop = 0.2 * rnorm(n);
+
+# data matrices
+snps.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop;
+gene.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop + snps.mat*((1:ngs)/ngs)^9/2;
+
+# data objects for Matrix eQTL engine
+snps1 = SlicedData$new( t( snps.mat ) );
+gene1 = SlicedData$new( t( gene.mat ) );
+cvrt1 = SlicedData$new();
+rm(snps.mat, gene.mat);
+
+# Slice data in blocks of 500 variables
+snps1$ResliceCombined(500);
+gene1$ResliceCombined(500);
+
+# Produce no output files
+filename = NULL; # tempfile()
+
+# Perform analysis recording information for a Q-Q plot
+me = Matrix_eQTL_main(
+	snps = snps1, 
+	gene = gene1, 
+	cvrt = cvrt1, 
+	output_file_name = filename,
+	pvOutputThreshold = 1e-6, 
+	useModel = modelLINEAR, 
+	errorCovariance = numeric(), 
+	verbose = TRUE,
+	pvalue.hist = "qqplot");
+
+# png(filename = "QQplot.png", width = 650, height = 650);
+plot(me, pch = 16, cex = 0.7, ylim = c(0,11));
+# dev.off();