Generics for Embbedding Pathway Analysis Results into a SummarizedExperiment Object — utils-SummarizedExperiment • iSEEpathways

An overview of the generics for embedding pathway analysis results into a SummarizedExperiment object, in a format compatible with iSEEpathways.

Usage

embedPathwaysResults(x, se, name, pathwayType, ...)

embedPathwaysResultsMethods

# S4 method for class 'data.frame'
embedPathwaysResults(x, se, name, class, pathwayType, ...)

Format

embedPathwaysResultsMethods: Named character vector mapping keywords to class names designed to store pathway analysis results.

Arguments

x: Object to be embedded.
se: A SummarizedExperiment object.
name: Identifier for the embedded object.
pathwayType: Character scalar indicating the type of pathway. See Details.
...: Arguments passed to individual constructors of pathway analysis result classes.
class: Class to use for embedding x. Only used when class(x) does not uniquely identify the package that generated the object x.

Value

embedPathwaysResults returns an updated SummarizedExperiment object that contains the embedded object.

Details

The argument pathwayType= is used to identify the function mapping a certain type of pathway identifier to the corresponding feature identifiers. Pathway mapping functions must be registered as a named list using registerAppOptions(se, Pathways.map.functions = list(...)), where the name matching pathwayType identifies the function to use to map pathway identifiers to feature identifiers in a given pathway analysis result, e.g.

library(org.Hs.eg.db)
map_GO <- function(pathway_id) {
  mapIds(org.Hs.eg.db, pathway_id, "ENSEMBL", keytype = "GOALL", multiVals = "CharacterList")[[pathway_id]]
}
se <- registerAppOptions(se, Pathways.map.functions = list(GO = map_go))

See vignette("integration", package = "iSEEpathways") for examples.

Definitions

embedPathwaysResults(x, se, name, pathwayType, ...) embeds the results x in the SummarizedExperiment se under the key name; pathwayType is a character scalar required to identify a function mapping a pathway identifier to asssociated feature identifiers; additional named arguments in ... are passed to the constructor of the pathway results class.

Author

Kevin Rue-Albrecht

Examples

embedPathwaysResultsMethods
#>              fgsea 
#> "iSEEfgseaResults" 

showMethods(embedPathwaysResults)
#> Function: embedPathwaysResults (package iSEEpathways)
#> x="data.frame"
#> x="data.table"
#>     (inherited from: x="data.frame")
#> x="iSEEfgseaResults"
#>