MergeObjects | R Documentation |
Merge 2 different PathwayObjects
MergeObjects(Object.1, Object.2)
Object.1 |
A PathwayObject. |
Object.2 |
A PathwayObject. |
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.files.NoBCKGRND <- Great.files[!grepl("BCKGRND", Great.files)] Great.Object1 <- LoadGeneSets(file_location = Great.files.NoBCKGRND, groupnames= c("KO", "WT"), P.cutoff = 0.05, Mol.cutoff = 5, Source = "Great", Great.Background = FALSE, type = "Canonical_Pathways", topranks = 20, structure = "SYMBOL", Organism = "org.Mm.eg.db", seperator = ",") 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 = ",") GREAT.merged.object <- MergeObjects(Object.1 =Great.Object1, Object.2 = Great.bckgnrd.Object1)
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