View source: R/ManageGeneSets.R
ManageGeneSets | R Documentation |
Filter unwanted groups from the PathwayObject
ManageGeneSets(Object, exclude.type = "", keep.type = "")
Object |
A PathwayObject. |
exclude.type |
A vector with strings of groups meant to be removed from the PathwayObject while keeping all others. |
keep.type |
A vector with strings of groups meant to be kept from the PathwayObject removing all others. |
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="")
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