WriteGeneSets

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 = getwd(),
             name = "IPA_20181123", write = "Both")