View source: R/GetSTRINGdbPerGeneSets.R
GetSTRINGdbPerGeneSets | R Documentation |
GetSTRINGdbPerGeneSets
GetSTRINGdbPerGeneSets(Object, unique.per.cluster = T, plot.input = "All")
Object |
A PathwayObject. |
unique.per.cluster |
A vector with strings of genes within each Gene-Set. Each string is seperated using the seperator supplied. |
plot.input |
A vector with group names of the different gene set experiments |
a list with the string output and the prep for the plotting function PlotSTRINGdbPerGeneSets
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") StringObject_unique <- GetSTRINGdbPerGeneSets(Object = IPA.object3, unique.per.cluster = TRUE , plot.input = "All")
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