Co-expression Modules identification Tool

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Documentation for package ‘CEMiTool’ version 1.30.0

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

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