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MergeObjects
EwoudEwing edited this page May 10, 2019
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1 revision
Merge 2 different PathwayObjects
MergeObjects(Object.1, Object.2)
Object.1 A PathwayObject.
Object.2 A PathwayObject.
Value 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)
Example Script: Example
Step 1A: Loading the data
Step 1B: Creating an Object
Step 2: Combine and Cluster
Step 2B: User supplied distance function
Step 2C: Highlighting-Genes
Step 3: Exporting Data
Step 4: Functional Investigation
Video: Step-by-step user guide