CEMiTool-class: An S4 class to represent the CEMiTool analysis.

In csbl-usp/CEMiTool: Co-expression Modules identification Tool

An S4 class to represent the CEMiTool analysis.

Description

An S4 class to represent the CEMiTool analysis.

Slots

expression

Gene expression data.frame.

sample_annotation

Sample annotation data.frame.

fit_indices

data.frame containing scale-free model fit, soft-threshold and network parameters.

selected_genes

Character vector containing the names of genes selected for analysis

module

Genes in modules information data.frame.

enrichment

list with modules enrichment results for sample classes.

ora

Over-representation analysis results data.frame.

interactions

list containing gene interactions present in modules.

interaction_plot

list of ggplot graphs with module gene interactions.

profile_plot

list of ggplot graphs with gene expression profile per module.

enrichment_plot

ggplot graph for enrichment analysis results.

beta_r2_plot

ggplot graph with scale-free topology fit results for each soft-threshold.

mean_k_plot

ggplot graph with mean network connectivity.

barplot_ora

list of ggplot graphs with over-representation analysis results per module.

sample_tree_plot

gtable containing sample dendrogram with class labels and clinical data (if available in sample_annotation(cem)).

mean_var_plot

Mean x variance scatterplot.

hist_plot

Expression histogram.

qq_plot

Quantile-quantile plot.

sample_name_column

character string containing the name of the column with sample names in the annotation file.

class_column

character string containing the name of the column with class names in the annotation file.

mod_colors

character vector containing colors associated with each network module.

parameters

list containing analysis parameters.

adjacency

matrix containing gene adjacency values based on correlation

Examples

# Get example expression data
data(expr0)
# Initialize CEMiTool object with expression
cem <- new("CEMiTool", expression=expr0)

csbl-usp/CEMiTool documentation built on March 27, 2024, 5:14 a.m.