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

In fcoex: FCBF-based Co-Expression Networks for Single Cells

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.

fcoex documentation built on Nov. 8, 2020, 6:45 p.m.