checkup_GeneTonic {GeneTonic} | R Documentation |
Checking the input objects for GeneTonic, whether these are all set for running the app
checkup_GeneTonic(dds, res_de, res_enrich, annotation_obj)
dds |
A |
res_de |
A |
res_enrich |
A |
annotation_obj |
A |
Some suggestions on the requirements for each parameter are returned in the error messages.
Invisible NULL
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) checkup_GeneTonic(dds = dds_macrophage, res_de = res_de, res_enrich = res_enrich, annotation_obj = anno_df) # if all is fine, it should return an invisible NULL and a simple message