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')

[Package IRISFGM version 1.2.0 Index]