Co-expression Modules identification Tool


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Documentation for package ‘CEMiTool’ version 1.30.0

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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
cem CEMiTool Object
cemitool Full gene co-expression analysis
CEMiTool-class An S4 class to represent the CEMiTool analysis.
diagnostic_report Diagnostic report
diagnostic_report-method Diagnostic report
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
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
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
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
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
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
ora_data Retrieve over representation analysis (ORA) results
ora_data-method Retrieve over representation analysis (ORA) results
plot_beta_r2 Soft-threshold beta selection graph
plot_beta_r2-method Soft-threshold beta selection graph
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
read_gmt Read a GMT file
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
write_files Save the CEMiTool object in files
write_files-method Save the CEMiTool object in files