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1 \name{modelLINEAR}
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2 \alias{modelLINEAR}
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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 = modelLINEAR} in the call of \code{\link{Matrix_eQTL_main}} to indicate that the effect of genotype on expression should be assumed to be additive linear.
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9 }
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10
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11 \examples{
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12 library('MatrixEQTL')
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13
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14 # Number of columns (samples)
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15 n = 100;
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16
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17 # Number of covariates
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18 nc = 10;
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19
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20 # Generate the standard deviation of the noise
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21 noise.std = 0.1 + rnorm(n)^2;
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22
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23 # Generate the covariates
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24 cvrt.mat = 2 + matrix(rnorm(n*nc), ncol = nc);
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25
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26 # Generate the vectors with genotype and expression variables
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27 snps.mat = cvrt.mat \%*\% rnorm(nc) + rnorm(n);
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28 gene.mat = cvrt.mat \%*\% rnorm(nc) + rnorm(n) * noise.std + 0.5 * snps.mat + 1;
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29
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30 # Create 3 SlicedData objects for the analysis
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31 snps1 = SlicedData$new( matrix( snps.mat, nrow = 1 ) );
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32 gene1 = SlicedData$new( matrix( gene.mat, nrow = 1 ) );
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33 cvrt1 = SlicedData$new( t(cvrt.mat) );
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34
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35 # name of temporary output file
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36 filename = tempfile();
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37
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38 # Call the main analysis function
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39 me = Matrix_eQTL_main(
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40 snps = snps1,
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41 gene = gene1,
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42 cvrt = cvrt1,
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43 output_file_name = filename,
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44 pvOutputThreshold = 1,
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45 useModel = modelLINEAR,
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46 errorCovariance = diag(noise.std^2),
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47 verbose = TRUE,
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48 pvalue.hist = FALSE );
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49 # remove the output file
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50 unlink( filename );
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51
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52 # Pull Matrix eQTL results - t-statistic and p-value
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53 beta = me$all$eqtls$beta;
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54 tstat = me$all$eqtls$statistic;
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55 pvalue = me$all$eqtls$pvalue;
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56 rez = c(beta = beta, tstat = tstat, pvalue = pvalue)
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57 # And compare to those from the linear regression in R
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58 {
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59 cat('\n\n Matrix eQTL: \n');
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60 print(rez);
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61 cat('\n R summary(lm()) output: \n');
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62 lmodel = lm( gene.mat ~ snps.mat + cvrt.mat, weights = 1/noise.std^2 );
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63 lmout = summary( lmodel )$coefficients[2, c(1,3,4)];
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64 print( lmout )
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65 }
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66
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67 # Results from Matrix eQTL and 'lm' must agree
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68 stopifnot(all.equal(lmout, rez, check.attributes=FALSE))
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69 }
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70 \references{
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71 The package website: \url{http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/}
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72 }
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73 \seealso{
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74 See \code{\link{Matrix_eQTL_engine}} for reference and sample code.
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75 }
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