checkup_gtl {GeneTonic} | R Documentation |
gtl
input object for GeneTonicChecking the gtl
("GeneTonic list") input object for GeneTonic, with the
correct content and format expected
checkup_gtl(gtl, verbose = FALSE)
gtl |
A
|
verbose |
Logical, to control level of verbosity of the messages generated |
Some suggestions on the requirements for the gtl
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) gtl <- list( dds = dds_macrophage, res_de = res_de, res_enrich = res_enrich, annotation_obj = anno_df ) checkup_gtl(gtl) # if all is fine, it should return an invisible NULL and a simple message