plot_volcano: Volcano plot differential expression results'

In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

Volcano plot differential expression results'

Description

The plot colors genes where the adjusted p-value exceed the 'p_value_threshold' and the 'fold_change_threshold'. Optionally, provide a list of genes to label in the plot via 'gene_list'.

Usage

plot_volcano(de, p_value_threshold, fold_change_threshold, gene_list)

Arguments

de	Differential expression results from "sageseqr::differential_expression()" output object named "differential_expression".
p_value_threshold	Numeric. P-values are adjusted by Benjamini and Hochberg (BH) false discovery rate (FDR). Significant genes are those with an adjusted p-value greater than this threshold.
fold_change_threshold	Numeric. Significant genes are those with a fold-change greater than this threshold.
gene_list	A vector of genes to label in the volcano plot.

Sage-Bionetworks/sageseqr documentation built on June 13, 2024, 2:11 p.m.