RunPathway {IRISFGM}

R Documentation

RunPathway

Description

This function will perform enrichment analysis based on a gene module or identified differentially expressed genes (DEG). This function is also depended on clusterProfiler, AnnotationDbi, org.Mm.eg.db, and org.Hs.eg.db package.

Usage

RunPathway(object, ...)

.runPathway(
  object = NULL,
  N.bicluster = c(10, 11, 12, 13),
  selected.gene.cutoff = 0.05,
  species = "Human",
  database = "GO",
  genes.source = c("CTS", "Bicluster")
)

## S4 method for signature 'IRISFGM'
RunPathway(
  object = NULL,
  N.bicluster = c(10, 11, 12, 13),
  selected.gene.cutoff = 0.05,
  species = "Human",
  database = "GO",
  genes.source = c("CTS", "Bicluster")
)

Arguments

object	Input IRIS-FGM object
...	other arguments passed to methods
N.bicluster	Select the numebr of bicluster to perform this function.
selected.gene.cutoff	Set up a statistical significance cutoff for all identified DEGs.
species	You can choose either 'Human' or 'Mouse'
database	You can choose either 'GO' or 'KEGG' database
genes.source	You can choose a gene list source, either 'CTS' or 'Bicluster.' 'CTS' means from cell-type-specific DEGs, and 'Bicluster means using gene module from the selected bicluster.'

Value

It will reture a function enrichment analysis.

Examples

# To rum this function based on the gene module from an identified bicluster use: 
data("example_object")
# due to execute time for this function, please use the function below

object <- RunPathway(object = example_object, 
 N.bicluster = 4, 
 selected.gene.cutoff = 0.05,
 species = 'Human', database = 'GO', genes.source = 'Bicluster')

---