GeneTonic_list {GeneTonic} | R Documentation |
Create a list for GeneTonic from the single required components.
GeneTonic_list(dds, res_de, res_enrich, annotation_obj)
dds |
A |
res_de |
A |
res_enrich |
A
|
annotation_obj |
A |
Having this dedicated function saves the pain of remembering which names the components of the list should have.
A GeneTonic
-list object, containing in its named slots the arguments
specified above: dds
, res_de
, res_enrich
, and annotation_obj
- the names
of the list are specified following the requirements for using it as single
input to GeneTonic()
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) gtl_macrophage <- GeneTonic_list( dds = dds_macrophage, res_de = res_de, res_enrich = res_enrich, annotation_obj = anno_df ) # now everything is in place to launch the app if (interactive()) { GeneTonic(gtl = gtl_macrophage) }