Part 3: Exporting data

Export the combined pathways and RR

We can say we want just the clustered pathways, or we want to have a look at both the RR and the clustered pathways. It writes it in the folder assigned to file_location and it takes the name of Name and writes it into a CSV file with seperation of “;”, to make it readable by Excel.

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")

Links

WriteGeneSets