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1 \name{modelANOVA}
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2 \alias{modelANOVA}
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3 \docType{data}
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4 \title{
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5 Constant for \code{\link{Matrix_eQTL_engine}}.
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6 }
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7 \description{
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8 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.
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9 }
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10 \note{
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11 By default, the number of ANOVA categories is fixed to be 3.
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12
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13 To set it to a different number (say, 4) use the following command:
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14
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15 \code{options(MatrixEQTL.ANOVA.categories=4)}
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16
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17 To check the current settings run:
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18
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19 \code{getOption('MatrixEQTL.ANOVA.categories', 3);}
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20 }
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21 \examples{
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22 library('MatrixEQTL')
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23
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24 # Number of columns (samples)
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25 n = 100;
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26
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27 # Number of covariates
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28 nc = 10;
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29
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30 # Generate the standard deviation of the noise
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31 noise.std = 0.1 + rnorm(n)^2;
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32
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33 # Generate the covariates
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34 cvrt.mat = 2 + matrix(rnorm(n*nc), ncol = nc);
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35
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36 # Generate the vectors with single genotype and expression variables
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37 snps.mat = floor(runif(n, min = 0, max = 3));
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38 gene.mat = 1 + (snps.mat==1) + cvrt.mat \%*\% rnorm(nc) + rnorm(n) * noise.std;
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39
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40 # Create 3 SlicedData objects for the analysis
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41 snps1 = SlicedData$new( matrix( snps.mat, nrow = 1 ) );
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42 gene1 = SlicedData$new( matrix( gene.mat, nrow = 1 ) );
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43 cvrt1 = SlicedData$new( t(cvrt.mat) );
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44
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45 # name of temporary output file
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46 filename = tempfile();
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47
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48 snps1
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49 gene1
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50
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51 # Call the main analysis function
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52 me = Matrix_eQTL_main(
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53 snps = snps1,
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54 gene = gene1,
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55 cvrt = cvrt1,
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56 output_file_name = filename,
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57 pvOutputThreshold = 1,
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58 useModel = modelANOVA,
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59 errorCovariance = diag(noise.std^2),
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60 verbose = TRUE,
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61 pvalue.hist = FALSE );
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62 # remove the output file
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63 unlink( filename );
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64
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65 # Pull Matrix eQTL results - t-statistic and p-value
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66
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67 fstat = me$all$eqtls$statistic;
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68 pvalue = me$all$eqtls$pvalue;
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69 rez = c( Fstat = fstat, pvalue = pvalue)
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70 # And compare to those from ANOVA in R
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71 {
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72 cat('\n\n Matrix eQTL: \n');
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73 print(rez);
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74 cat('\n R anova(lm()) output: \n')
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75 lmodel = lm( gene.mat ~ cvrt.mat + factor(snps.mat), weights = 1/noise.std^2 );
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76 lmout = anova( lmodel )[2, 4:5];
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77 print( lmout )
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78 }
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79
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80 # Results from Matrix eQTL and 'lm' must agree
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81 stopifnot(all.equal(lmout, rez, check.attributes=FALSE))
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82 }
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83 \references{
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84 The package website: \url{http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/}
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85 }
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86 \seealso{
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87 See \code{\link{Matrix_eQTL_engine}} for reference and sample code.
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88 }
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