### R code from vignette source 'OGSAUsersManual.Rnw' ################################################### ### code chunk number 1: Load format setup ################################################### library('OGSA') data('ExampleData') data('KEGG_BC_GS') phenotype <- pheno names(phenotype) <- colnames(cnv) tailLRL <- c('left','right','left') tailRLR <- c('right','left','right') offsets <- c(1.0, 0.1, 0.5) dataSet <- list(expr,meth,cnv) ################################################### ### code chunk number 2: Process Gene Sets ################################################### tibLRL <- copaInt(dataSet,phenotype,tails=tailLRL) gsTibLRL <- testGScogps(tibLRL,pathGS) tibLRLcorr <- copaInt(dataSet,phenotype,tails=tailLRL,corr=TRUE) gsTibLRLcorr <- testGScogps(tibLRLcorr,pathGS) tibRLR <- copaInt(dataSet,phenotype,tails=tailRLR) tibRLRcorr <- copaInt(dataSet,phenotype,tails=tailRLR,corr=TRUE) gsTibRLR <- testGScogps(tibRLR,pathGS) gsTibRLRcorr <- testGScogps(tibRLRcorr,pathGS) rankLRL <- copaInt(dataSet,phenotype,tails=tailLRL,method='Rank') rankLRLcorr <- copaInt(dataSet,phenotype,tails=tailLRL,method='Rank',corr=TRUE, offsets=offsets) gsRankLRL <- testGScogps(rankLRL,pathGS) gsRankLRLcorr <- testGScogps(rankLRLcorr,pathGS) rankRLR <- copaInt(dataSet,phenotype,tails=tailRLR,method='Rank') rankRLRcorr <- copaInt(dataSet,phenotype,tails=tailRLR,method='Rank',corr=TRUE, offsets=offsets) gsRankRLR <- testGScogps(rankRLR,pathGS) gsRankRLRcorr <- testGScogps(rankRLRcorr,pathGS) ################################################### ### code chunk number 3: Process Outlier Maps ################################################### outRankLRLcorr <- outCallRank(dataSet, phenotype, names=c('Expr','Meth','CNV'),tail=tailLRL, corr=TRUE,offsets=offsets) outRankRLRcorr <- outCallRank(dataSet, phenotype, names=c('Expr','Meth','CNV'),tail=tailRLR, corr=TRUE,offsets=offsets) print("Corrected Rank Outliers Calculated") outTibLRL <- outCallTib(dataSet, phenotype, names=c('Expr','Meth','CNV'),tail=tailLRL) outTibRLR <- outCallTib(dataSet, phenotype, names=c('Expr','Meth','CNV'),tail=tailRLR) print("Tibshirani-Hastie Outliers Calculated") pdgfB <- pathGS$'BIOCARTA_PDGF_PATHWAY' map1 <- outMap(outTibLRL,pdgfB,hmName='BC_PDGF_TIB.pdf', plotName='PDGF Outlier T-H LRL Calls') ecmK <- pathGS$'KEGG_ECM_RECEPTOR_INTERACTION' map4 <- outMap(outRankRLRcorr,ecmK,hmName='KEGG_ECM_RANKcorr.pdf', plotName='ECM Outlier Corr Rank RLR Calls')