## ----DEA_one_pack, echo=TRUE, results="hide", message=FALSE, warning=FALSE---- library(ExpHunterSuite) data(toc) data(target) degh_out_one_pack <- main_degenes_Hunter(raw=toc, target=target, modules="D") # D for DESeq2 ## ----input_data, echo=TRUE, results="as.is", message=FALSE, warning=FALSE----- head(toc) head(target) ## ----input_files, echo=TRUE, results="as.is"---------------------------------- system.file("extData", "table_of_counts.txt", package = "ExpHunterSuite") system.file("extData", "target.txt", package = "ExpHunterSuite") ## ----DEA_multi_pack, echo=TRUE, results="hide", message=FALSE, warning=FALSE---- degh_out_multi_pack <- main_degenes_Hunter(raw=toc, target=target, modules="DEL") # D:DESeq2 E:EdgeR, L:limma ## ----standard_DEA_results, echo=TRUE------------------------------------------ head(degh_out_multi_pack$DE_all_genes) ## ----standard_DEA_model_target, echo=TRUE, results="as.is"-------------------- target_multi <- data.frame(target, age_group = c("adult", "child", "adult", "child", "adult", "adult", "child")) target_multi ## ----standard_DEA_model_execute, results="hide", message=FALSE, warning=FALSE---- degh_out_model <- main_degenes_Hunter(raw=toc, target=target_multi, modules="D", model_variables="age_group") ## ----standard_CEA, results="hide", message=FALSE, warning=FALSE--------------- degh_out_coexp <- main_degenes_Hunter(raw=toc, target=target_multi, modules="DW", string_factors="age_group") ## ----standard_FA, results="as.is", eval=FALSE-------------------------------- # # fh_out_one_pack <- main_functional_hunter( #Perform enrichment analysis # degh_out_one_pack, # model_organism = 'Mouse', # Use specified organism database # enrich_dbs = c("MF", "BP", "CC", "Kegg", "Reactome"), # Enrichment analysis for GO, KEGG and Reactome # enrich_methods = "o" # Use overepresentation analysis only # ) # ## ----coexp_FA, results="as.is", eval=FALSE------------------------------------ # # fh_out_coexp <- main_functional_hunter( # Perform enrichment analisys # degh_out_coexp, # model_organism = 'Mouse', # Use specified organism database # enrich_dbs = c("MF", "BP", "CC", "Kegg", "Reactome"), # Enrichment analysis for GO, KEGG and Reactome # enrich_methods = "o" # Use overepresentation analysi only # ) # ## ----c2e, echo=TRUE, eval=FALSE, results="hide"------------------------------ # input_file <- system.file("extData", "cluster_genes.txt", package = "ExpHunterSuite") # print(readLines(input_file,n=2)) # # organisms_table <- get_organism_table() # current_organism_info <- organisms_table[rownames(organisms_table) %in% "Mouse",] # org_db <- get_org_db(current_organism_info) # # enr_lists <- main_clusters_to_enrichment(input_file, org_db=org_db, # current_organism_info=current_organism_info, gene_keytype="ENSEMBL") ## ----write_reports, echo=TRUE, eval=FALSE, results="hide"--------------------- # # write_expression_report(exp_results=degh_out_coexp) # write_enrich_files(func_results=fh_out_one_pack) # write_functional_report(hunter_results=degh_out_coexp, # func_results=fh_out_coexp)