background


        require(GCModeller);
                               

#' tools for handling GSEA background model.
imports "background" from "gseakit";

.NET clr type export
metpa: metpa	metpa symbol
gsea_background: Background	a collection of the functional related gene consist of this background model. (假设基因组是有许多个功能聚类的集合构成的)
gene_symbol: BackgroundGene	a member gene in a gsea cluster model, or a symbol reference to the target object.

.NET clr function exports
as.data.frame.background	Background: a collection of the functional related gene consist of this background model. (假设基因组是有许多个功能聚类的集合构成的)
clusterIDs	get all of the cluster id set from the given background model object
moleculeIDs	get all of the molecule id set from the given background model object
meta_background
dag.background	create gsea background from a given obo ontology file data.
append.id_terms	Append id terms to a given gsea background
background.id_mapping	do id mapping of the members in the background cluster
read.background	Load GSEA background model from a xml file.
write.background	Save GSEA background model as xml file
cut_background
background_summary	summary of the background model as dataframe
clusterInfo	get cluster info data table
geneSet.annotations	make gene set annotation via a given gsea background model
geneSet.intersects	get an intersection id list between the background model and the given gene id list.
geneSet.filter	make filter of the background model
KO.table	convert the background model to a data table
gsea_cluster	Create a cluster for gsea background
metpa	Create the gsea background model for metabolism analysis
fromList	cast the cluster data as the enrichment background
as.background	cast the cluster data as the enrichment background
KO_reference	gene/protein KO id background
as.geneSet	Extract the gene set list from the background model
metabolism.background	create kegg maps background for the metabolism data analysis
compoundBrite	get kegg compound class brite background model
KO.background	create kegg background model