## ----setup, include = FALSE---------------------------------------------- knitr::opts_chunk$set(cache=TRUE) ## ----eval = FALSE-------------------------------------------------------- # library(devtools) # install_github("billyhw/GSALightning") ## ------------------------------------------------------------------------ library(GSALightning) ## ------------------------------------------------------------------------ data(expression) data(sampleInfo) ## ------------------------------------------------------------------------ data(targetGenes) ## ------------------------------------------------------------------------ expression <- expression[apply(expression,1,sd) != 0,] ## ------------------------------------------------------------------------ GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = 1000, minsize = 10, rmGSGenes = 'gene') head(GSALightResults) ## ----eval=FALSE---------------------------------------------------------- # ? GSALight ## ------------------------------------------------------------------------ data(expression) expression[1:4,1:3] ## ------------------------------------------------------------------------ data(sampleInfo) head(sampleInfo$TN) ## ------------------------------------------------------------------------ data(targetGenes) targetGenes[1:3] ## ----error=TRUE---------------------------------------------------------- data(expression) data(sampleInfo) data(targetGenes) GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes) ## ----error=TRUE---------------------------------------------------------- expression <- expression[apply(expression,1,sd) != 0,] GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes) ## ------------------------------------------------------------------------ GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = 1000, rmGSGenes = 'gene') head(GSALightResults) ## ------------------------------------------------------------------------ GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = 1000, method = 'maxmean', restandardize = FALSE, minsize = 10, maxsize = 30, rmGSGenes = 'gene', verbose = FALSE) ## ------------------------------------------------------------------------ GSALightResultsMean <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = 1000, method = 'mean', restandardize = FALSE, minsize = 10, maxsize = 30, rmGSGenes = 'gene', verbose = FALSE) ## ------------------------------------------------------------------------ GSALightResultsAbs <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = 1000, method = 'absmean', restandardize = FALSE, minsize = 10, maxsize = 30, rmGSGenes = 'gene', verbose = FALSE) ## ------------------------------------------------------------------------ head(GSALightResults) head(GSALightResultsMean) ## ------------------------------------------------------------------------ head(GSALightResultsAbs) ## ------------------------------------------------------------------------ GSALightResults <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = NULL, method = 'maxmean', restandardize = FALSE, minsize = 10, rmGSGenes = 'gene', verbose = FALSE) ## ------------------------------------------------------------------------ hist(GSALightResults[,'p-value:up-regulated in Control'], main=NULL, xlab='p-value') ## ------------------------------------------------------------------------ GSALightResultsReStand <- GSALight(eset = expression, fac = factor(sampleInfo$TN), gs = targetGenes, nperm = NULL, method = 'maxmean', restandardize = TRUE, minsize = 10, rmGSGenes = 'gene', verbose = FALSE) hist(GSALightResultsReStand[,'p-value:up-regulated in Control'], main=NULL, xlab='p-value') ## ------------------------------------------------------------------------ GSALightResultsReStand[order(GSALightResultsReStand[,'p-value:up-regulated in Control'],decreasing=F)[1:10], c(2,4)] ## ------------------------------------------------------------------------ singleGeneAnalysis <- permTestLight(eset = expression, fac = factor(sampleInfo$TN), nperm = 1000, method = 'mean', verbose = TRUE) head(singleGeneAnalysis) ## ------------------------------------------------------------------------ singleWilcox <- wilcoxTest(eset = expression, fac = factor(sampleInfo$TN), tests = "unpaired") head(singleWilcox) ## ------------------------------------------------------------------------ fac <- 1:(ncol(expression)/2) fac <- c(fac, -fac) head(fac) tail(fac) ## ------------------------------------------------------------------------ GSALightResultsPaired <- GSALight(eset = expression, fac = fac, gs = targetGenes, nperm = 1000, tests = 'paired', method = 'maxmean', restandardize = TRUE, minsize = 10, rmGSGenes = 'gene', verbose = FALSE) head(GSALightResultsPaired)