RunPathway {IRISFGM} | R Documentation |
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.
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") )
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.' |
It will reture a function enrichment analysis.
# 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')