--- a +++ b/NAMESPACE @@ -0,0 +1,61 @@ +# Generated by roxygen2: do not edit by hand + +S3method(plot,bioTMLE) +export(.biotmle) +export(biomarkertmle) +export(eif) +export(heatmap_ic) +export(modtest_ic) +export(rnaseq_ic) +export(toptable) +export(volcano_ic) +exportClasses(bioTMLE) +exportClasses(data.frame_OR_EList) +import(BiocGenerics) +importClassesFrom(S4Vectors,Annotated) +importClassesFrom(S4Vectors,Vector) +importClassesFrom(SummarizedExperiment,SummarizedExperiment) +importClassesFrom(limma,EList) +importClassesFrom(methods,data.frame) +importFrom(BiocParallel,MulticoreParam) +importFrom(BiocParallel,bplapply) +importFrom(BiocParallel,bpprogressbar) +importFrom(BiocParallel,register) +importFrom(SummarizedExperiment,SummarizedExperiment) +importFrom(SummarizedExperiment,assay) +importFrom(SummarizedExperiment,colData) +importFrom(SummarizedExperiment,rowData) +importFrom(assertthat,assert_that) +importFrom(dplyr,"%>%") +importFrom(dplyr,arrange) +importFrom(dplyr,filter) +importFrom(dplyr,mutate) +importFrom(dplyr,select) +importFrom(dplyr,slice) +importFrom(drtmle,drtmle) +importFrom(ggplot2,aes) +importFrom(ggplot2,geom_histogram) +importFrom(ggplot2,geom_point) +importFrom(ggplot2,ggplot) +importFrom(ggplot2,ggtitle) +importFrom(ggplot2,guide_legend) +importFrom(ggplot2,guides) +importFrom(ggplot2,theme_bw) +importFrom(ggplot2,xlab) +importFrom(ggplot2,ylab) +importFrom(ggsci,scale_fill_gsea) +importFrom(limma,eBayes) +importFrom(limma,lmFit) +importFrom(limma,topTable) +importFrom(limma,voom) +importFrom(limma,voomWithQualityWeights) +importFrom(methods,is) +importFrom(methods,new) +importFrom(methods,setClass) +importFrom(methods,setClassUnion) +importFrom(stats,p.adjust) +importFrom(stats,plogis) +importFrom(stats,quantile) +importFrom(superheat,superheat) +importFrom(tibble,as_tibble) +importFrom(tibble,rownames_to_column)