GenesPerGeneSet-PathwayObject-method: GenesPerGeneSet

In TranslationalBioinformaticsUnit/GeneSetCluster: Cluster together Gene-Sets from Gene Set Analysis

GenesPerGeneSet

Description

GenesPerGeneSet

Usage

## S4 method for signature 'PathwayObject'
GenesPerGeneSet(Object)

Arguments

Object	a PathwayObject
PathwayObject	a PathwayObject

Value

dataframe of pathwayobjects

Examples

IPA.files <- c(system.file("extdata",
                           "MM10.IPA.KO.uGvsMac.Canonical_pathways.xls",
                            package = "GeneSetCluster"),
             system.file("extdata",
                            "MM10.IPA.WT.uGvsMac.Canonical_pathways.xls",
                             package = "GeneSetCluster"),
             system.file("extdata",
                             "MM10.IPA.KO.uGvsMac.Functional_annotations.xls",
                             package = "GeneSetCluster"),
             system.file("extdata",
                             "MM10.IPA.WT.uGvsMac.Functional_annotations.xls",
                             package = "GeneSetCluster"))
canonical.files <- IPA.files[grep("Canonical", IPA.files)]

IPA.object1 <- LoadGeneSets(file_location = canonical.files,
                         groupnames= c("KO", "WT"),
                         P.cutoff = 1.3,
                         Mol.cutoff = 5,
                         Source = "IPA",
                         type = "Canonical_Pathways",
                         structure = "SYMBOL",
                         seperator = ",")
IPA.object2 <- CombineGeneSets(Object = IPA.object1)
IPA.object3 <- ClusterGeneSets(Object = IPA.object2,
                              clusters = 7,
                              method = "kmeans")
GenesPerGeneSet(Object =IPA.object3 )

TranslationalBioinformaticsUnit/GeneSetCluster documentation built on Feb. 2, 2023, 4:06 a.m.