--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MatrixEQTL/demo/sample.all.r	Fri Mar 12 08:12:46 2021 +0000
@@ -0,0 +1,96 @@
+# Matrix eQTL by Andrey A. Shabalin
+# http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/
+# 
+# Be sure to use an up to date version of R and Matrix eQTL.
+
+# source("Matrix_eQTL_R/Matrix_eQTL_engine.r");
+library(MatrixEQTL)
+
+## Location of the package with the data files.
+base.dir = find.package('MatrixEQTL');
+# base.dir = '.';
+
+## Settings
+
+# Linear model to use, modelANOVA, modelLINEAR, or modelLINEAR_CROSS
+useModel = modelLINEAR; # modelANOVA, modelLINEAR, or modelLINEAR_CROSS
+
+# Genotype file name
+SNP_file_name = paste(base.dir, "/data/SNP.txt", sep="");
+
+# Gene expression file name
+expression_file_name = paste(base.dir, "/data/GE.txt", sep="");
+
+# Covariates file name
+# Set to character() for no covariates
+covariates_file_name = paste(base.dir, "/data/Covariates.txt", sep="");
+
+# Output file name
+output_file_name = tempfile();
+
+# Only associations significant at this level will be saved
+pvOutputThreshold = 1e-2;
+
+# Error covariance matrix
+# Set to numeric() for identity.
+errorCovariance = numeric();
+# errorCovariance = read.table("Sample_Data/errorCovariance.txt");
+
+
+## Load genotype data
+
+snps = SlicedData$new();
+snps$fileDelimiter = "\t";      # the TAB character
+snps$fileOmitCharacters = "NA"; # denote missing values;
+snps$fileSkipRows = 1;          # one row of column labels
+snps$fileSkipColumns = 1;       # one column of row labels
+snps$fileSliceSize = 2000;      # read file in slices of 2,000 rows
+snps$LoadFile(SNP_file_name);
+
+## Load gene expression data
+
+gene = SlicedData$new();
+gene$fileDelimiter = "\t";      # the TAB character
+gene$fileOmitCharacters = "NA"; # denote missing values;
+gene$fileSkipRows = 1;          # one row of column labels
+gene$fileSkipColumns = 1;       # one column of row labels
+gene$fileSliceSize = 2000;      # read file in slices of 2,000 rows
+gene$LoadFile(expression_file_name);
+
+## Load covariates
+
+cvrt = SlicedData$new();
+cvrt$fileDelimiter = "\t";      # the TAB character
+cvrt$fileOmitCharacters = "NA"; # denote missing values;
+cvrt$fileSkipRows = 1;          # one row of column labels
+cvrt$fileSkipColumns = 1;       # one column of row labels
+if(length(covariates_file_name)>0) {
+	cvrt$LoadFile(covariates_file_name);
+}
+
+## Run the analysis
+
+me = Matrix_eQTL_engine(
+		snps = snps,
+		gene = gene,
+		cvrt = cvrt,
+		output_file_name = output_file_name,
+		pvOutputThreshold = pvOutputThreshold,
+		useModel = useModel, 
+		errorCovariance = errorCovariance, 
+		verbose = TRUE,
+		pvalue.hist = TRUE,
+		min.pv.by.genesnp = FALSE,
+		noFDRsaveMemory = FALSE);
+
+unlink(output_file_name);
+
+## Results:
+
+cat('Analysis done in: ', me$time.in.sec, ' seconds', '\n');
+cat('Detected eQTLs:', '\n');
+show(me$all$eqtls)
+
+## Plot the histogram of all p-values
+
+plot(me)