GeneTonic {GeneTonic} | R Documentation |
GeneTonic, main function for the Shiny app
GeneTonic(dds, res_de, res_enrich, annotation_obj, project_id = "")
dds |
A |
res_de |
A |
res_enrich |
A
|
annotation_obj |
A |
project_id |
A character string, which can be considered as an identifier
for the set/session, and will be e.g. used in the title of the report created
via |
A Shiny app object is returned, for interactive data exploration
Federico Marini
library("macrophage") library("DESeq2") library("org.Hs.eg.db") library("AnnotationDbi") # dds object data("gse", package = "macrophage") dds_macrophage <- DESeqDataSet(gse, design = ~line + condition) rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15) dds_macrophage <- estimateSizeFactors(dds_macrophage) # annotation object anno_df <- data.frame( gene_id = rownames(dds_macrophage), gene_name = mapIds(org.Hs.eg.db, keys = rownames(dds_macrophage), column = "SYMBOL", keytype = "ENSEMBL"), stringsAsFactors = FALSE, row.names = rownames(dds_macrophage) ) # res object data(res_de_macrophage, package = "GeneTonic") res_de <- res_macrophage_IFNg_vs_naive # res_enrich object data(res_enrich_macrophage, package = "GeneTonic") res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive) res_enrich <- get_aggrscores(res_enrich, res_de, anno_df) # now everything is in place to launch the app if (interactive()) GeneTonic(dds = dds_macrophage, res_de = res_de, res_enrich = res_enrich, annotation_obj = anno_df, project_id = "myexample")