--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MatrixEQTL/man/modelANOVA.Rd	Fri Mar 12 08:12:46 2021 +0000
@@ -0,0 +1,88 @@
+\name{modelANOVA}
+\alias{modelANOVA}
+\docType{data}
+\title{
+	Constant for \code{\link{Matrix_eQTL_engine}}.
+}
+\description{
+	Set parameter \code{useModel = modelANOVA} in the call of \code{\link{Matrix_eQTL_main}} to indicate that the genotype should be treated as a categorical variable.
+}
+\note{
+By default, the number of ANOVA categories is fixed to be 3.
+
+To set it to a different number (say, 4) use the following command:
+
+\code{options(MatrixEQTL.ANOVA.categories=4)}
+
+To check the current settings run:
+
+\code{getOption('MatrixEQTL.ANOVA.categories', 3);}
+}
+\examples{
+library('MatrixEQTL')	
+			
+# Number of columns (samples)
+n = 100;
+
+# Number of covariates
+nc = 10;
+
+# Generate the standard deviation of the noise
+noise.std = 0.1 + rnorm(n)^2;
+
+# Generate the covariates
+cvrt.mat = 2 + matrix(rnorm(n*nc), ncol = nc);
+
+# Generate the vectors with single genotype and expression variables
+snps.mat = floor(runif(n, min = 0, max = 3));
+gene.mat = 1 + (snps.mat==1) + cvrt.mat \%*\% rnorm(nc) + rnorm(n) * noise.std;
+
+# Create 3 SlicedData objects for the analysis
+snps1 = SlicedData$new( matrix( snps.mat, nrow = 1 ) );
+gene1 = SlicedData$new( matrix( gene.mat, nrow = 1 ) );
+cvrt1 = SlicedData$new( t(cvrt.mat) );
+
+# name of temporary output file
+filename = tempfile();
+
+snps1
+gene1
+
+# Call the main analysis function
+me = Matrix_eQTL_main(
+  snps = snps1, 
+  gene = gene1, 
+  cvrt = cvrt1, 
+  output_file_name = filename, 
+  pvOutputThreshold = 1, 
+  useModel = modelANOVA, 
+  errorCovariance = diag(noise.std^2), 
+  verbose = TRUE,
+  pvalue.hist = FALSE );
+# remove the output file
+unlink( filename );
+
+# Pull Matrix eQTL results - t-statistic and p-value
+
+fstat = me$all$eqtls$statistic;
+pvalue = me$all$eqtls$pvalue;
+rez = c( Fstat = fstat, pvalue = pvalue)
+# And compare to those from ANOVA in R
+{
+  cat('\n\n Matrix eQTL: \n'); 
+  print(rez);
+  cat('\n R anova(lm()) output: \n')
+  lmodel = lm( gene.mat ~ cvrt.mat + factor(snps.mat), weights = 1/noise.std^2 );
+  lmout = anova( lmodel )[2, 4:5];
+  print( lmout )
+}
+
+# Results from Matrix eQTL and 'lm' must agree
+stopifnot(all.equal(lmout, rez, check.attributes=FALSE))
+}
+\references{
+	The package website: \url{http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/}
+}
+\seealso{
+	See \code{\link{Matrix_eQTL_engine}} for reference and sample code.
+}