## ----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 <- functional_hunter( #Perform enrichment analysis # degh_out_one_pack, # 'Mouse', # Use specified organism database # func_annot_db = "gKR", # Enrichment analysis for GO, KEGG and Reactome # GO_subont = "BMC", # analysis_type= "o" # Use overepresentation analysis only (Not GSEA) # ) # fh_out_coexp <- functional_hunter( # Perform enrichment analisys # degh_out_coexp, # 'Mouse', # Use specified organism database # func_annot_db = "gKR", # Enrichment analysis for GO, KEGG and Reactome # GO_subont = "BMC", # analysis_type= "o" # Use overepresentation analysi only (Not GSEA) # ) ## ----write_reports, echo=TRUE, eval=FALSE------------------------------------- # print(getwd()) # 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) ## ----input_files_cl, echo=TRUE, results="hide"-------------------------------- input_toc <- system.file("extdata", "table_of_counts.txt", package = "mypackage") input_toc input_target <- system.file("extdata", "target.txt", package = "mypackage") input_target