enrichPATH: Method to enrich results from differential studies on KEGG...

In isglobal-brge/postRexposome: Package to enrich exposome-omic data analyis results.

Description

This method takes a ResultSet and performs an enrichment on KEGG pathways or GO terms in base to a given set of genes. Argument database allows to select the database where the query will be performed. sel.pval allows to select the column of the resulting table in ResultSet with the p-value to be used in the process. Argument th.pval is used to exclude features using sel.pval column. Argument sel.feature indicates the column that has the gene associated to the feature (row in the table of results). feature.id indicates the coding system for the sel.feature column.

Usage

enrichPATH(object, rid = 1, fData.tag = 1, version = c("hg18", "hg19"),
  database = c("KEGG", "GO:CC", "GO:BP", "GO:MF"), sel.pval = c("P.Value",
  "adj.P.Val"), th.pval = 0.01, sel.feature = "genes",
  feature.id = "geneSymbol", feature.null = "", plot.fit = FALSE,
  verbose = FALSE, warnings = TRUE)

Arguments

object	Object of class ResultSet.
rid	(default 1) If given ResultSet that has more than one result, id to select the result where the enrichment will be performed.
fData.tag	(default 1) Identifier of the annotation to be used to mach the probes of ResultSet with gene identifier. In other words, index of the element in fData that matches the omic dataset to be used in the enrichment.
version	(default "hg18") Can takes "hg18" and "hg19" and corresponds to the genome version to use for enrichment in KEGG/GO.
database	(default "KEGG") Can takes values "KEGG", "GO:CC", "GO:BP" and "GO:MF"; corresponding to the available enrichments.
sel.pval	(default "adj.P.Val") Name of the P.Value columns to filter datset's probes given th.pval.
th.pval	(default 0.01) Threshold used to include a probe (CpG) into the enrichment analysis.
sel.feature	(default "genes") Name containing gene identifier in ResultSet's fData.
feature.id	(default "geneSymbol") Name of the format of the gene identifier. Run supportedGeneIDs from geneLenDataBase for more information. This must match with the identifier in ResultSet's fData.
feature.null	(default "") String identifier for non gene-assigned probes.
plot.fit	(default FALSE) If set to TRUE calls plot PWF with default values.
verbose	(default FALSE) If set to TRUE messages indicating the steps done by the method are raised.
warnings	(default TRUE) If set to FALSE important notes raised by the method are hide.

Note

The Gene Ontology Consortium; Gene Ontology Consortium: going forward; Nucl Acids Res (2015).

Ashburner et al.; Gene ontology: tool for the unification of biology; Nat Genet (2000).

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K; KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res (2017).

Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res (2016).

Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

isglobal-brge/postRexposome documentation built on May 18, 2019, 5:50 a.m.