# FCBF-based Co-Expression Networks for Single Cells

## Documentation for package ‘fcoex’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.get_correlates | .get_correlates
.plot_one_interaction | Network visualization
discretize | Set the discretized expression attribute Uses the discretize_exprs function of the FCBF package
discretize-method | Set the discretized expression attribute Uses the discretize_exprs function of the FCBF package
fc | Example fcoex object
fcoex-class | An S4 class to represent the fcoex analysis.
find_cbf_modules | find_cbf_modules
find_cbf_modules-method | find_cbf_modules
get_nets | Network visualization
get_nets-method | Network visualization
idents | Retrieves module identities from the recluster function
idents-method | Retrieves module identities from the recluster function
mini_pbmc3k | Processed subset of the pbmc3k dataset from PBMC genomics
module_genes | Get the module genes in a fcoex object
module_genes-method | Get the module genes in a fcoex object
mod_colors | Set module colors mod_colors attribute
mod_colors-method | Set module colors mod_colors attribute
mod_gene_num | Get the number of genes in modules in a fcoex object This function was copied and adapted from the CEMiTool package.
mod_gene_num-method | Get the number of genes in modules in a fcoex object This function was copied and adapted from the CEMiTool package.
mod_names | Get module names in a fcoex object
mod_names-method | Get module names in a fcoex object
mod_ora | # Run module overrepresentation analysis
mod_ora-method | # Run module overrepresentation analysis
new_fcoex | Create a fcoex object
nmodules | Get the number of modules in a fcoex object
nmodules-method | Get the number of modules in a fcoex object
ora_data | Retrieve over representation analysis (ORA) results
ora_data-method | Retrieve over representation analysis (ORA) results
plot_ora | ORA visualization
plot_ora-method | ORA visualization
recluster | Recluster cells based on fcoex module composition
recluster-method | Recluster cells based on fcoex module composition
save_plots | Save fcoex object plots
save_plots-method | Save fcoex object plots
show-method | Print a fcoex object
show_net | Retrieve fcoex net plots
show_net-method | Retrieve fcoex net plots
show_ora | Retrieve fcoex ora plots
show_ora-method | Retrieve fcoex ora plots