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multimodalR/NAMESPACE
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Checked and updated all functions Added multiple filtering functions Added functions to process TCGA data Added data to exclude genes on allosomes Checked & updated vignettes Changed Package name to multimodalR Added function to check for valid unified output data format Added function to plot Survival Curves for TCGA data Added function to check for known bimodal genes in output First Complete Version of multimodalR
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| # Generated by roxygen2: do not edit by hand | |
| export(cleanOutput) | |
| export(evaluateAlgorithmOutput) | |
| export(filter0sumGenes) | |
| export(filterForFoldChange) | |
| export(filterForKnownInCancer) | |
| export(filterForMean) | |
| export(filterForXChromosomeGenes) | |
| export(filterForYChromosomeGenes) | |
| export(filterMultimodalGenes) | |
| export(filterRarelyExpressedGenes) | |
| export(getClassifications) | |
| export(getFilteredData) | |
| export(getParam) | |
| export(getParams) | |
| export(getStatistics) | |
| export(isValidUnifiedOutputDataFormat) | |
| export(newParams) | |
| export(plotClassifications) | |
| export(plotExpression) | |
| export(plotOutput) | |
| export(plotStatistics) | |
| export(plotSurvivalCurves) | |
| export(processOneCancerGroup) | |
| export(setParam) | |
| export(setParams) | |
| export(simulateExpression) | |
| export(toCancerDataGroups) | |
| export(updateGeneNames) | |
| export(useDiptest) | |
| export(useFlexmix) | |
| export(useHdbscan) | |
| export(useMclust) | |
| export(useSilvermantest) | |
| exportClasses(Params) | |
| import(flexmix) | |
| import(mclust) | |
| importFrom(KEGGREST,keggGet) | |
| importFrom(LaplacesDemon,rinvgaussian) | |
| importFrom(biomaRt,getBM) | |
| importFrom(biomaRt,useMart) | |
| importFrom(checkmate,assertCharacter) | |
| importFrom(checkmate,assertClass) | |
| importFrom(checkmate,assertList) | |
| importFrom(checkmate,assertString) | |
| importFrom(cowplot,add_sub) | |
| importFrom(cowplot,ggdraw) | |
| importFrom(diptest,dip.test) | |
| importFrom(doParallel,registerDoParallel) | |
| importFrom(dplyr,mutate) | |
| importFrom(dplyr,select) | |
| importFrom(foreach,"%dopar%") | |
| importFrom(foreach,foreach) | |
| importFrom(ggkm,geom_km) | |
| importFrom(ggplot2,aes) | |
| importFrom(ggplot2,coord_fixed) | |
| importFrom(ggplot2,element_text) | |
| importFrom(ggplot2,facet_wrap) | |
| importFrom(ggplot2,geom_bar) | |
| importFrom(ggplot2,geom_density) | |
| importFrom(ggplot2,ggplot) | |
| importFrom(ggplot2,ggtitle) | |
| importFrom(ggplot2,labs) | |
| importFrom(ggplot2,scale_color_discrete) | |
| importFrom(ggplot2,scale_fill_manual) | |
| importFrom(ggplot2,stat_function) | |
| importFrom(ggplot2,theme) | |
| importFrom(ggplot2,theme_bw) | |
| importFrom(ggplot2,xlab) | |
| importFrom(ggplot2,ylab) | |
| importFrom(grDevices,dev.off) | |
| importFrom(grDevices,grey.colors) | |
| importFrom(grDevices,pdf) | |
| importFrom(graphics,hist) | |
| importFrom(graphics,par) | |
| importFrom(magrittr,"%>%") | |
| importFrom(methods,"slot<-") | |
| importFrom(methods,new) | |
| importFrom(methods,rbind2) | |
| importFrom(methods,slot) | |
| importFrom(methods,slotNames) | |
| importFrom(methods,validObject) | |
| importFrom(parallel,clusterEvalQ) | |
| importFrom(parallel,clusterExport) | |
| importFrom(parallel,detectCores) | |
| importFrom(parallel,makeCluster) | |
| importFrom(parallel,parLapply) | |
| importFrom(parallel,stopCluster) | |
| importFrom(plyr,compact) | |
| importFrom(reshape2,melt) | |
| importFrom(reticulate,import) | |
| importFrom(silvermantest,silverman.test) | |
| importFrom(stats,BIC) | |
| importFrom(stats,as.formula) | |
| importFrom(stats,dnorm) | |
| importFrom(stats,pchisq) | |
| importFrom(stats,rgamma) | |
| importFrom(stats,rnorm) | |
| importFrom(stats,runif) | |
| importFrom(stats,sd) | |
| importFrom(stringr,str_replace_all) | |
| importFrom(survival,Surv) | |
| importFrom(survival,survdiff) | |
| importFrom(utils,combn) | |
| importFrom(utils,head) |