Co-expression Modules identification Tool
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Documentation for package ‘CEMiTool’ version 1.33.0
Help Pages
| 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 |