RunORA {scDiffCom} | R Documentation |
Run over-representation analysis
Description
Perform over-representation analysis (ORA) on a scDiffCom object, with the possibility to define new categories in addition to the standard ones supported by default.
Usage
RunORA(
object,
categories = c("LRI", "LIGAND_COMPLEX", "RECEPTOR_COMPLEX", "ER_CELLTYPES",
"EMITTER_CELLTYPE", "RECEIVER_CELLTYPE", "GO_TERMS", "KEGG_PWS"),
extra_annotations = NULL,
overwrite = TRUE,
verbose = TRUE
)
## S4 method for signature 'scDiffCom'
RunORA(
object,
categories = c("LRI", "LIGAND_COMPLEX", "RECEPTOR_COMPLEX", "ER_CELLTYPES",
"EMITTER_CELLTYPE", "RECEIVER_CELLTYPE", "GO_TERMS", "KEGG_PWS"),
extra_annotations = NULL,
overwrite = TRUE,
verbose = TRUE
)
Arguments
object |
|
categories |
Names of the standard categories on which to perform ORA.
Default is all standard categories, namely
|
extra_annotations |
Convenience parameter to perform ORA on user-defined
non-standard categories. If |
overwrite |
If |
verbose |
If |
Details
Additional user-defined ORA categories can be added via the
parameter extra_annotations
. The data.frames or data.tables in this
list must have exactly two columns that indicates a relationship between
values from a standard category (first column) to values of the new
category (second column). As a typical example, this
vignette
shows how to perform ORA on cell type families attached to each cell type.
Value
A scDiffCom object with updated slot ora_table
.