# Co-expression Modules identification Tool

## Documentation for package ‘CEMiTool’ version 1.6.11

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

## Help Pages

A C D E F G I M N O P R S W

## -- A --

adj_data | Get or set adjacency matrix value
adj_data-method | Get or set adjacency matrix value
adj_data<- | Get or set adjacency matrix value
adj_data<--method | Get or set adjacency matrix value

## -- C --

cem | CEMiTool Object
cemitool | Full gene co-expression analysis
CEMiTool-class | An S4 class to represent the CEMiTool analysis.
cem_overlap | Integrates CEMiTool analyses

## -- D --

diagnostic_report | Diagnostic report
diagnostic_report-method | Diagnostic report

## -- E --

enrich_mods | Enriches communities
expr0 | Yellow Fever gene expression data from GEO study GSE13485
expr_data | Retrieve and set expression attribute
expr_data-method | Retrieve and set expression attribute
expr_data<- | Retrieve and set expression attribute
expr_data<--method | Retrieve and set expression attribute

## -- F --

filter_genes | Filter a gene expression data.frame
find_modules | Co-expression modules definition
find_modules-method | Co-expression modules definition
fit_data | Retrieve scale-free model fit data
fit_data-method | Retrieve scale-free model fit data

## -- G --

generate_report | CEMiTool report
generate_report-method | CEMiTool report
get_adj | Calculate adjacency matrix
get_adj-method | Calculate adjacency matrix
get_beta_data | Soft-threshold beta data
get_beta_data-method | Soft-threshold beta data
get_cemitool_r2_beta | Calculate CEMiTool beta and R2 values
get_cemitool_r2_beta-method | Calculate CEMiTool beta and R2 values
get_connectivity | Calculate network connectivity
get_connectivity-method | Calculate network connectivity
get_hubs | Get hubs
get_hubs-method | Get hubs
get_merged_mods | Merge similar modules
get_merged_mods-method | Merge similar modules
get_mods | Calculate co-expression modules
get_mods-method | Calculate co-expression modules
get_phi | Calculate phi
get_phi-method | Calculate phi
gsea_data | Retrieve Gene Set Enrichment Analysis (GSEA) results
gsea_data-method | Retrieve Gene Set Enrichment Analysis (GSEA) results

## -- I --

interactions_data | Retrieve and set interaction data to CEMiTool object
interactions_data-method | Retrieve and set interaction data to CEMiTool object
interactions_data<- | Retrieve and set interaction data to CEMiTool object
interactions_data<--method | Retrieve and set interaction data to CEMiTool object

## -- M --

module_genes | Get the module genes in a CEMiTool object
module_genes-method | Get the module genes in a CEMiTool object
mod_colors | Retrieve and set mod_colors attribute
mod_colors-method | Retrieve and set mod_colors attribute
mod_colors<- | Retrieve and set mod_colors attribute
mod_colors<--method | Retrieve and set mod_colors attribute
mod_gene_num | Get the number of genes in modules in a CEMiTool object
mod_gene_num-method | Get the number of genes in modules in a CEMiTool object
mod_gsea | Module Gene Set Enrichment Analysis
mod_gsea-method | Module Gene Set Enrichment Analysis
mod_names | Get module names in a CEMiTool object
mod_names-method | Get module names in a CEMiTool object
mod_ora | Module Overrepresentation Analysis
mod_ora-method | Module Overrepresentation Analysis
mod_summary | Co-expression module summarization
mod_summary-method | Co-expression module summarization

## -- N --

new_cem | Create a CEMiTool object
nmodules | Get the number of modules in a CEMiTool object
nmodules-method | Get the number of modules in a CEMiTool object

## -- O --

ora_data | Retrieve over representation analysis (ORA) results
ora_data-method | Retrieve over representation analysis (ORA) results
overlap_community | Generates communities from edgelist

## -- P --

plot_beta_r2 | Soft-threshold beta selection graph
plot_beta_r2-method | Soft-threshold beta selection graph
plot_comembership | Plot module edge co-membership
plot_consensus | Plot graph of consensus modules
plot_gsea | GSEA visualization
plot_gsea-method | GSEA visualization
plot_hist | Plot histogram
plot_hist-method | Plot histogram
plot_interactions | Network visualization
plot_interactions-method | Network visualization
plot_mean_k | Network mean connectivity
plot_mean_k-method | Network mean connectivity
plot_mean_var | Plot mean and variance
plot_mean_var-method | Plot mean and variance
plot_ora | ORA visualization
plot_ora-method | ORA visualization
plot_profile | Expression profile visualization
plot_profile-method | Expression profile visualization
plot_qq | Plot quantile-quantile plot
plot_qq-method | Plot quantile-quantile plot
plot_sample_tree | Sample clustering
plot_sample_tree-method | Sample clustering
plot_similarity | Plot study module similarity

## -- R --

read_gmt | Read a GMT file

## -- S --

sample_annot | Yellow Fever Sample Annotation data
sample_annotation | Retrive or set the sample_annotation attribute
sample_annotation-method | Retrive or set the sample_annotation attribute
sample_annotation<- | Retrive or set the sample_annotation attribute
sample_annotation<--method | Retrive or set the sample_annotation attribute
save_plots | Save CEMiTool object plots
save_plots-method | Save CEMiTool object plots
select_genes | Select genes based on variance
show-method | Print a cemitool object
show_plot | Retrieve CEMiTool object plots
show_plot-method | Retrieve CEMiTool object plots
stat_overlap_mods | Calculate module overlap statistics

## -- W --

write_files | Save the CEMiTool object in files
write_files-method | Save the CEMiTool object in files