{background} R# Documentation

background


require(GCModeller);

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

tools for handling GSEA background model.

.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
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
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

background_summary
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.

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

as.background

cast the cluster data as the enrichment background

KO_reference

gene/protein KO id background

as.geneSet
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


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