R/01_AllMethods.R

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

#' Method to enrich results from differential studies on DisGeNET database
#' 
#' This method takes the results from a \code{ResultSet} and uses the genes
#' associated to the probes to perform a query in DisGeNET and obtain the
#' diseases associated to the given genes.
#' 
#' @param object Object of class \code{ResultSet}.
#' @param rid (default \code{1}) If given \code{ResultSet} hat has more than 
#' one result, id to select the result where the enrichment will be performed.
#' @param fData.tag (default \code{1}) Identifier of the annotation to be
#' used to mach the probes of \code{ResultSet} with gene identifier. In other
#' words, index of the element in \code{fData} that matches the omic dataset 
#' to be used in the enrichment.
#' @param sel.pval (default \code{"adj.P.Val"}) Name of the P.Value columns to 
#' filter datset's probes given \code{th.pval}.
#' @param th.pval (default \code{0.01}) Threshold used to include a probe (CpG)
#' into the enrichment analysis.
#' @param sel.feature (default \code{"genes"}) Name containing gene identifier
#' in \code{ResultSet}'s \code{fData}.
#' @param feature.null (default \code{""}) String identifier for non 
#' gene-assigned probes.
#' @param database (default \code{"CURATED"}) Name of the version of the
#' DisGeNET's databse where the query will be computed. Check 
#' \code{?disgenetGene} for a description of each name.
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} messages
#' indicating the steps done by the method are raised.
#' @param warnings (default \code{TRUE}) If set to \code{FALSE} important
#' notes raised by the method are hide.
#' @export enrichDIS
#' @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
setGeneric("enrichDIS", function(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)
    standardGeneric("enrichDIS")
)

#' Method to enrich in anatomical terms provided by Bgee Database
#' 
#' TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO TODO
#' 
#' @param object Object of class \code{ResultSet}.
#' @param rid (default \code{1}) If given \code{ResultSet} hat has more than 
#' one result, id to select the result where the enrichment will be performed.
#' @param fData.tag (default \code{1}) Identifier of the annotation to be
#' used to mach the probes of \code{ResultSet} with gene identifier. In other
#' words, index of the element in \code{fData} that matches the omic dataset 
#' to be used in the enrichment.
#' @param sel.pval (default \code{"adj.P.Val"}) Name of the P.Value columns to 
#' filter datset's probes given \code{th.pval}.
#' @param th.pval (default \code{0.01}) Threshold used to include a probe (CpG)
#' into the enrichment analysis.
#' @param sel.feature (default \code{"genes"}) Name containing gene identifier
#' in \code{ResultSet}'s \code{fData}.
#' @param feature.null (default \code{""}) String identifier for non 
#' gene-assigned probes.
#' @param bgee.data (default \code{"affymetrix"}) Type of data requested to 
#' Bgee to perform the functinal enrichment. Can take any of them or more than
#' one of the possibles options.
#' @param statistic (default \code{"fisher"}) Statistic used to test the
#' enrichment in Bgee anatomical categories throught \code{topGO} R package.
#' Check \code{whichTests()} for available tests.
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} messages
#' indicating the steps done by the method are raised.
#' @param warnings (default \code{TRUE}) If set to \code{FALSE} important
#' notes raised by the method are hide.
#' @export enrichANAT
#' @note 
#' Komljenovic A, Roux J, Robinson-Rechavi M, Bastian F;
#' BgeeDB, an R package for retrieval of curated expression datasets and for 
#' gene list enrichment tests. 
#' F1000Research (2016).
#' 
#' Bastian F, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M;
#' Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among 
#' Species; Data Integration Life Sci. Lecture Notes in Computer Science (2008)
#' @examples 
#' data(air)
#' ans <- enrichANAT(air, rid="NO2", sel.pval="P.Value", warnings=FALSE,
#'     sel.feature="gene_assignment", translate.from="REFSEQ")
#' ans
setGeneric("enrichANAT", function(object, rid=1, coef=2, contrast=1,
                                  fData.tag=2, sel.pval="adj.P.Val", th.pval=0.01, 
                                  sel.feature="genes", feature.null=c("", "---"), translate.from=NA,
                                  bgee.data="affymetrix", statistic="fisher", verbose=FALSE, warnings=TRUE)
    standardGeneric("enrichANAT")
)

#' Method to enrich results from differential studies on KEGG and GO 
#' databases
#' 
#' This method takes a \code{ResultSet} and performs an enrichment on KEGG
#' pathways or GO terms in base to a given set of genes. Argument 
#' \code{database} allows to select the database where the query will be 
#' performed. \code{sel.pval} allows to select the column of the resulting
#' table in \code{ResultSet} with the p-value to be used in the process.
#' Argument \code{th.pval} is used to exclude features using \code{sel.pval}
#' column. Argument \code{sel.feature} indicates the column that has the
#' gene associated to the feature (row in the table of results).
#' \code{feature.id} indicates the coding system for the \code{sel.feature}
#' column.
#' 
#' @param object Object of class \code{ResultSet}.
#' @param rid (default \code{1}) If given \code{ResultSet} that has more than 
#' one result, id to select the result where the enrichment will be performed.
#' @param fData.tag (default \code{1}) Identifier of the annotation to be
#' used to mach the probes of \code{ResultSet} with gene identifier. In other
#' words, index of the element in \code{fData} that matches the omic dataset 
#' to be used in the enrichment.
#' @param version (default \code{"hg18"}) Can takes \code{"hg18"} and 
#' \code{"hg19"} and corresponds to the genome version to use for enrichment 
#' in KEGG/GO.
#' @param database (default \code{"KEGG"}) Can takes values \code{"KEGG"}, 
#' \code{"GO:CC"}, \code{"GO:BP"} and \code{"GO:MF"}; corresponding to 
#' the available enrichments.
#' @param sel.pval (default \code{"adj.P.Val"}) Name of the P.Value columns to 
#' filter datset's probes given \code{th.pval}.
#' @param th.pval (default \code{0.01}) Threshold used to include a probe (CpG)
#' into the enrichment analysis.
#' @param sel.feature (default \code{"genes"}) Name containing gene identifier
#'  in \code{ResultSet}'s \code{fData}.
#' @param feature.id (default \code{"geneSymbol"}) Name of the format of the 
#' gene identifier. Run \link{supportedGeneIDs} from \code{geneLenDataBase} for 
#' more information. This must match with the identifier in \code{ResultSet}'s 
#' \code{fData}.
#' @param feature.null (default \code{""}) String identifier for non 
#' gene-assigned probes.
#' @param plot.fit (default \code{FALSE}) If set to \code{TRUE} calls plot 
#' \link{PWF} with default values.
#' @param verbose (default \code{FALSE}) If set to \code{TRUE} messages
#' indicating the steps done by the method are raised.
#' @param warnings (default \code{TRUE}) If set to \code{FALSE} important
#' notes raised by the method are hide.
#' @export enrichPATH
#' @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).
setGeneric("enrichPATH", function(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)
    standardGeneric("enrichPATH")
)