WriteGeneSets: WriteGeneSets

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

WriteGeneSets

Description

Exports the pathways into a csv file

Usage

WriteGeneSets(Object, file_location = "~/Project9/test/",
  name = "IPA_20181123", write = "Both")

Arguments

Object	is a PathwayObject.
file_location	where to write the files to
name	name to be added to the files, what experiments are these
write	what to write, either "Data", "RR" or "Both"

Value

written tables in the folder designated.

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 = 12,
                              method = "kmeans")
#WriteGeneSets(Object= IPA.object3,
 #           file_location = "~/Project9/test/",
 #            name = "IPA_20181123", write = "Both")

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