ORAGeneSets | R Documentation |
ORAGeneSets
ORAGeneSets(Object, ORA.returned = 10, unique.per.cluster = T)
Object |
A PathwayObject. |
ORA.returned |
A numeric for how Go terms should be returned per analysis. Alternative use "All" to get all of them. |
unique.per.cluster |
A vector with strings of genes within each Gene-Set. Each string is seperated using the seperator supplied. |
a data frame with the over represented gene sets for all the clusters.
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, #where are the files groupnames= c("KO", "WT"),#Names of the groups 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") ORAGeneSets(Object = IPA.object3,unique.per.cluster = TRUE , ORA.returned = 1)
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