View source: R/HighlightGeneSets.R
HighlightGeneSets | R Documentation |
Adds a highlight score if the Gene-Set overlaps with a gene subset which is supplied by the user.
HighlightGeneSets(Object, highligt.genes, name = "Ros")
Object |
A PathwayObject. |
highligt.genes |
A vector with genes from the subset the user is interested in. e.g. a list of ROS genes. |
name |
The name of the subset which will be added to the score calculated. |
a pathwayobject
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") system.file("data", "Redox.genes.rda", package = "testdat") IPA.object3.highlight <- HighlightGeneSets(Object = IPA.object3, highligt.genes = Redox.genes, name = "Ros")
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