View source: R/CombineGeneSets.R
CombineGeneSets | R Documentation |
Calculate distances between the different experiments.
CombineGeneSets(Object, combineMethod = "Standard", combineMethod.supplied, display = "Condensed")
Object |
A PathwayObject. |
combineMethod |
lets the functions know if the standard RR, a Jaccard index or Cohens Kappa. |
combineMethod.supplied |
a function which parameter A and parameter B. |
display |
Either Condensed or Expanded. Expanded seperates the groups and adds a 1 to every group is this molecular signature is seen here |
a pathwayobject
Great.files <- c(system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed.tsv", package = "GeneSetCluster"), system.file("extdata", "MM10.GREAT.KO.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster"), system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed.tsv", package = "GeneSetCluster"), system.file("extdata", "MM10.GREAT.WT.uGvsMac.bed_BCKGRND.tsv", package = "GeneSetCluster")) Great.files.bckgrnd <- Great.files[grepl("BCKGRND", Great.files)] Great.bckgnrd.Object1 <- LoadGeneSets(file_location = Great.files.bckgrnd, groupnames= c("KO", "WT"), P.cutoff = 0.05, Mol.cutoff = 5, Source = "Great", Great.Background = TRUE, type = "Canonical_Pathways", topranks = 20, structure = "SYMBOL", Organism = "org.Mm.eg.db", seperator = ",") man.Great.Object1 <- ManageGeneSets(Object = Great.bckgnrd.Object1, keep.type =c("Disease Ontology", "GO Biological Process" ), exclude.type="") man.Great.Object2 <- CombineGeneSets(Object = man.Great.Object1)
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