## ----setup, include=FALSE------------------------------------------------ library(knitr) opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center") ## ----lib, warning=FALSE, message=FALSE, results="hide"------------------- library(BioQC) ## ----gmt----------------------------------------------------------------- gmtFile <- system.file("extdata/test.gmt", package="BioQC") ## print the file context cat(readLines(gmtFile), sep="\n") ## read the file into SignedGenesets genesets <- readSignedGmt(gmtFile) print(genesets) ## ----gmtPos-------------------------------------------------------------- genesets <- readSignedGmt(gmtFile, nomatch="pos") print(genesets) ## ----data---------------------------------------------------------------- set.seed(1887) testN <- 100L testSampleCount <- 3L testGenes <- c("AKT1", "AKT2", "ERBB2", "ERBB3", "EGFR","TSC1", "TSC2", "GATA2", "GATA4", "GATA1", "GATA3") testRows <- c(testGenes, paste("Gene", (length(testGenes)+1):testN, sep="")) testMatrix <- matrix(rnorm(testN*testSampleCount, sd=0.1), nrow=testN, dimnames=list(testRows, NULL)) testMatrix[1:2,] <- testMatrix[1:2,]+10 testMatrix[6:7,] <- testMatrix[6:7,]-10 testMatrix[3:4,] <- testMatrix[3:4,]-5 testMatrix[5,] <- testMatrix[5,]+5 testEset <- new("ExpressionSet", exprs=testMatrix) ## ----index--------------------------------------------------------------- testIndex <- matchGenes(genesets, testEset, col=NULL) print(testIndex) ## ----runWmwGreater------------------------------------------------------- wmwResult.greater <- wmwTest(testEset, testIndex, valType="p.greater") print(wmwResult.greater) ## ----runWmwLess---------------------------------------------------------- wmwResult.less <- wmwTest(testEset, testIndex, valType="p.less") print(wmwResult.less) ## ----runWmwTwoSided------------------------------------------------------ wmwResult.two.sided <- wmwTest(testEset, testIndex, valType="p.two.sided") print(wmwResult.two.sided) ## ----runWmwQ------------------------------------------------------------- wmwResult.Q <- wmwTest(testEset, testIndex, valType="Q") print(wmwResult.Q) ## ----session------------------------------------------------------------- sessionInfo()