Mercurial > repos > jasonxu > matrixeqtl

comparison MatrixEQTL/demo/q.qqplot.r @ 0:cd4c8e4a4b5b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jasonxu
date Fri, 12 Mar 2021 08:12:46 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:cd4c8e4a4b5b
1 library("MatrixEQTL")
2
3 # Number of samples
4 n = 100;
5
6 # Number of variables
7 ngs = 2000;
8
9 # Common signal in all variables (population stratification)
10 pop = 0.2 * rnorm(n);
11
12 # data matrices
13 snps.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop;
14 gene.mat = matrix(rnorm(n*ngs), ncol = ngs) + pop + snps.mat*((1:ngs)/ngs)^9/2;
15
16 # data objects for Matrix eQTL engine
17 snps1 = SlicedData$new( t( snps.mat ) );
18 gene1 = SlicedData$new( t( gene.mat ) );
19 cvrt1 = SlicedData$new();
20 rm(snps.mat, gene.mat);
21
22 # Slice data in blocks of 500 variables
23 snps1$ResliceCombined(500);
24 gene1$ResliceCombined(500);
25
26 # Produce no output files
27 filename = NULL; # tempfile()
28
29 # Perform analysis recording information for a Q-Q plot
30 me = Matrix_eQTL_main(
31 snps = snps1,
32 gene = gene1,
33 cvrt = cvrt1,
34 output_file_name = filename,
35 pvOutputThreshold = 1e-6,
36 useModel = modelLINEAR,
37 errorCovariance = numeric(),
38 verbose = TRUE,
39 pvalue.hist = "qqplot");
40
41 # png(filename = "QQplot.png", width = 650, height = 650);
42 plot(me, pch = 16, cex = 0.7, ylim = c(0,11));
43 # dev.off();