--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MatrixEQTL/man/plot.MatrixEQTL.Rd	Fri Mar 12 08:12:46 2021 +0000
@@ -0,0 +1,112 @@
+\name{plot.MatrixEQTL}
+\alias{plot.MatrixEQTL}
+\title{Plot histogram or QQ-plot of all p-values
+}
+\description{
+This method plots a histogram or QQ-plot of p-values
+for all tests performed by \code{\link{Matrix_eQTL_engine}}.
+}
+\usage{
+\method{plot}{MatrixEQTL}(x, cex = 0.5, pch = 19, xlim = NULL, ylim = NULL,...)
+}
+\arguments{
+	\item{x}{
+		An object returned by \code{\link{Matrix_eQTL_engine}}.
+	}
+	\item{cex}{
+		A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
+	}
+	\item{pch}{
+		Plotting "character", i.e., symbol to use. See \code{\link[graphics]{points}}.
+	}
+	\item{xlim}{
+		Set the range of the horisontal axis.
+	}
+	\item{ylim}{
+		Set the range of the vertical axis.
+	}
+	\item{\dots}{
+		further graphical parameters passed to \code{\link[graphics]{lines}} and \code{\link[graphics]{points}}.
+	}
+}
+\details{
+	The plot type (histogram vs. QQ-plot) is determined by the \code{pvalue.hist} parameter in the call of \code{\link{Matrix_eQTL_engine}} function.
+}
+\value{
+	The method does not return any value.
+}
+\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.
+}
+\note{
+	The sample code below produces figures like these:
+	
+	Histogram: \figure{histogram.png}
+		
+	QQ-plot: \figure{QQplot.png}
+}
+\author{
+	Andrey Shabalin \email{ashabalin@vcu.edu}
+}
+\examples{
+library(MatrixEQTL)
+
+# Number of samples
+n = 100; 
+
+# Number of variables
+ngs = 2000;
+
+# Common signal in all variables
+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 histogram
+meh = Matrix_eQTL_engine(
+    snps = snps1, 
+    gene = gene1, 
+    cvrt = cvrt1, 
+    output_file_name = filename, 
+    pvOutputThreshold = 1e-100, 
+    useModel = modelLINEAR, 
+    errorCovariance = numeric(), 
+    verbose = TRUE,
+    pvalue.hist = 100);
+    
+plot(meh, col="grey")
+
+# Perform analysis recording information for a QQ-plot
+meq = Matrix_eQTL_engine(
+    snps = snps1, 
+    gene = gene1, 
+    cvrt = cvrt1, 
+    output_file_name = filename,
+    pvOutputThreshold = 1e-6, 
+    useModel = modelLINEAR, 
+    errorCovariance = numeric(), 
+    verbose = TRUE,
+    pvalue.hist = "qqplot");
+    
+plot(meq)
+}
+\keyword{ QQ-plot }
+\keyword{ histogram }