volcano_data: Data processing for volcano and ma plot

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Data processing for volcano and ma plot

Description

Data processing for volcano and ma plot

Usage

volcano_data(
  select_contrast,
  comparisons,
  top_genes,
  limma_p_val,
  limma_fc,
  processed_data,
  contrast_samples,
  all_gene_names,
  select_gene_id
)

Arguments

select_contrast	Comparison from DEG analysis to filter for the significant genes
comparisons	The comparisons vector from the results list of the limma_value function
top_genes	top_genes list from results list of the limma_value function
limma_p_val	Significant p-value to use to in determining the expressed genes
limma_fc	Minimum fold change value to use in determining the expressed genes
processed_data	Data matrix that has gone through pre-processing
contrast_samples	Samples that are included in the selected comparison
all_gene_names	Gene symbols, etc.
select_gene_id	Selected gene id type, symbol, Ensmembl, etc.

Value

A list containing processed data for volcano plot in plot_volcano() & plot_ma() and list of differently expressed genes for labeling

espors/idepGolem documentation built on Oct. 27, 2024, 4:56 a.m.