## ----include=FALSE, messages=FALSE, warnings=FALSE---------------------------- knitr::opts_chunk$set(comment="", fig.align="center", fig.width=8.75, cache=FALSE) library(devtools) library(tidyverse) library(magrittr) library(dplyr) library(reactable) devtools::load_all(".") ## ----------------------------------------------------------------------------- # Simply a character vector of symbols (hypergeometric) signature <- c("GENE1", "GENE2", "GENE3") # A ranked character vector of symbols (kstest) ranked.signature <- c("GENE2", "GENE1", "GENE3") # A ranked named numerical vector of symbols with ranking weights (gsea) weighted.signature <- c("GENE2"=1.22, "GENE1"=0.94, "GENE3"=0.77) ## ----------------------------------------------------------------------------- genesets <- list("GSET1" = c("GENE1", "GENE2", "GENE3"), "GSET2" = c("GENE4", "GENE5", "GENE6"), "GSET3" = c("GENE7", "GENE8", "GENE9")) ## ----eval=FALSE--------------------------------------------------------------- # BIOCARTA <- msigdb_gsets(species="Homo sapiens", category="C2", subcategory="CP:BIOCARTA") # KEGG <- msigdb_gsets(species="Homo sapiens", category="C2", subcategory="CP:KEGG") # REACTOME <- msigdb_gsets(species="Homo sapiens", category="C2", subcategory="CP:REACTOME") ## ----------------------------------------------------------------------------- hyp_obj <- hypeR(signature, genesets) ## ----------------------------------------------------------------------------- hyp_obj$info ## ----eval=FALSE--------------------------------------------------------------- # # Show interactive table # hyp_show(hyp_obj) # # # Plot dots plot # hyp_dots(hyp_obj) # # # Plot enrichment map # hyp_emap(hyp_obj) # # # Plot hiearchy map (relational genesets) # hyp_hmap(hyp_obj) # # # Map enrichment to an igraph object (relational genesets) # hyp_to_graph(hyp_obj) # # # Save to excel # hyp_to_excel(hyp_obj, file_path="hypeR.xlsx") # # # Save to table # hyp_to_table(hyp_obj, file_path="hypeR.txt") # # # Generate markdown report # hyp_to_rmd(hyp_obj, # file_path="hypeR.rmd", # title="Hyper Enrichment (hypeR)", # subtitle="YAP, TNF, and TAZ Knockout Experiments", # author="Anthony Federico, Stefano Monti")