enrichDIS: Method to enrich results from differential studies on...

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

Description

This method takes the results from a ResultSet and uses the genes associated to the probes to perform a query in DisGeNET and obtain the diseases associated to the given genes.

Usage

enrichDIS(object, rid = 1, coef = 2, contrast = 1, fData.tag = 2,
  sel.pval = "adj.P.Val", th.pval = 0.01, sel.feature = "gene",
  feature.null = c("", "---"), translate.from = NA, database = "CURATED",
  verbose = FALSE, warnings = TRUE)

Arguments

object	Object of class ResultSet.
rid	(default 1) If given ResultSet hat 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.
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.null	(default "") String identifier for non gene-assigned probes.
database	(default "CURATED") Name of the version of the DisGeNET's databse where the query will be computed. Check ?disgenetGene for a description of each name.
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

Pinero J, Queralt-Rosinach N, Bravo A, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI; DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes.; Database (2015).

Queralt-Rosinach N, Pinero J, Bravo A, Sanz F, Furlong LI; DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases Bioinformatics; Bioinformatics (2016).

Examples

data(air)
ans <- enrichDIS(air, rid="NO2", sel.pval="P.Value", warnings=FALSE,
    sel.feature="gene_assignment", translate.from="REFSEQ")
ans

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