CEMiTool-class {CEMiTool} | R Documentation

## 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)

[Package CEMiTool version 1.18.1 Index]