RunPathway: RunPathway

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

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

# If you want to perform this function based on identified DEGs, you should use: 
## Not run: object <- RunPathway(object = NULL,N.bicluster = NULL, selected.gene.cutoff = 0.05,
species = 'Human', database = 'GO', genes.source = 'CTS' 
## End(Not run)
# To rum this function based on the gene module from an identified bicluster use: 
## Not run: object <- RunPathway(object = NULL,N.bicluster = NULL, selected.gene.cutoff = 0.05,
species = 'Human', database = 'GO', genes.source = 'Bicluster' 
## End(Not run)

carter-allen/IRISFGM documentation built on Dec. 31, 2020, 9:54 p.m.