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1 \name{plot.MatrixEQTL}
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2 \alias{plot.MatrixEQTL}
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3 \title{Plot histogram or QQ-plot of all p-values
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4 }
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5 \description{
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6 This method plots a histogram or QQ-plot of p-values
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7 for all tests performed by \code{\link{Matrix_eQTL_engine}}.
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8 }
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9 \usage{
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10 \method{plot}{MatrixEQTL}(x, cex = 0.5, pch = 19, xlim = NULL, ylim = NULL,...)
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11 }
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12 \arguments{
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13 \item{x}{
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14 An object returned by \code{\link{Matrix_eQTL_engine}}.
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15 }
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16 \item{cex}{
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17 A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default.
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18 }
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19 \item{pch}{
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20 Plotting "character", i.e., symbol to use. See \code{\link[graphics]{points}}.
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21 }
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22 \item{xlim}{
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23 Set the range of the horisontal axis.
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24 }
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25 \item{ylim}{
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26 Set the range of the vertical axis.
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27 }
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28 \item{\dots}{
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29 further graphical parameters passed to \code{\link[graphics]{lines}} and \code{\link[graphics]{points}}.
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30 }
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31 }
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32 \details{
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33 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.
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34 }
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35 \value{
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36 The method does not return any value.
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37 }
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38 \references{
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39 The package website: \url{http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/}
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40 }
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41 \seealso{
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42 See \code{\link{Matrix_eQTL_engine}} for reference and sample code.
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43 }
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44 \note{
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45 The sample code below produces figures like these:
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46
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47 Histogram: \figure{histogram.png}
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48
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49 QQ-plot: \figure{QQplot.png}
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50 }
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51 \author{
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52 Andrey Shabalin \email{ashabalin@vcu.edu}
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53 }
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54 \examples{
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55 library(MatrixEQTL)
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56
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57 # Number of samples
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58 n = 100;
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59
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60 # Number of variables
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61 ngs = 2000;
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62
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63 # Common signal in all variables
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64 pop = 0.2*rnorm(n);
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65
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66 # data matrices
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67 snps.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop;
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68 gene.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop + snps.mat*((1:ngs)/ngs)^9/2;
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69
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70 # data objects for Matrix eQTL engine
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71 snps1 = SlicedData$new( t( snps.mat ) );
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72 gene1 = SlicedData$new( t( gene.mat ) );
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73 cvrt1 = SlicedData$new( );
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74 rm(snps.mat, gene.mat)
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75
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76 # Slice data in blocks of 500 variables
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77 snps1$ResliceCombined(500);
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78 gene1$ResliceCombined(500);
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79
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80 # Produce no output files
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81 filename = NULL; # tempfile()
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82
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83 # Perform analysis recording information for a histogram
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84 meh = Matrix_eQTL_engine(
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85 snps = snps1,
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86 gene = gene1,
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87 cvrt = cvrt1,
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88 output_file_name = filename,
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89 pvOutputThreshold = 1e-100,
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90 useModel = modelLINEAR,
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91 errorCovariance = numeric(),
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92 verbose = TRUE,
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93 pvalue.hist = 100);
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94
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95 plot(meh, col="grey")
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96
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97 # Perform analysis recording information for a QQ-plot
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98 meq = Matrix_eQTL_engine(
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99 snps = snps1,
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100 gene = gene1,
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101 cvrt = cvrt1,
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102 output_file_name = filename,
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103 pvOutputThreshold = 1e-6,
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104 useModel = modelLINEAR,
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105 errorCovariance = numeric(),
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106 verbose = TRUE,
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107 pvalue.hist = "qqplot");
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108
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109 plot(meq)
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110 }
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111 \keyword{ QQ-plot }
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112 \keyword{ histogram }
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