fcoex-class {fcoex} | R Documentation

## An S4 class to represent the fcoex analysis.

### Description

An S4 class to represent the fcoex analysis.

### Slots

`expression`

  Normalized gene expression table from single-cells `data.frame`.

`discretized_expression`

  Discretized gene expression table from single-cells `data.frame`.

`target`

  Original target classes for the cells (`factor`).

`selected_genes`

  Character `vector` containing the names of genes selected for analysis

`module_list`

  `list` containing genes in each module.

`adjacency`

  `data.frame` containing the adjacency table for the selected genes before trimming.

`adjacency_trimmed`

  `data.frame` containing the adjacency table for the selected genes after trimming.

`coex_network_plot`

  list of ggplot graphs with module gene interactions.

`new_clusters`

  `list` containing gene interactions present in modules.

`mod_colors`

  character `vector` containing colors associated with each network module.

`ora`

  Over-representation analysis results `data.frame`.

`barplot_ora`

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

`mod_idents`

  Identities of cells based on each co-expression module. Determined by the "recluster" method

`parameters`

  `list` containing analysis parameters.

[Package fcoex version 1.2.0 Index]