pdVolcano: pdVolcano

In genesofeve/projectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

pdVolcano

Description

Generate volcano plot and gate genes based on fold change and pvalue, includes vectors that can be used with fast gene set enrichment (fgsea)

Usage

pdVolcano(
  result,
  FC = 0.2,
  pvalue = NULL,
  subset = NULL,
  filter.inf = FALSE,
  label.num = 5L,
  display = TRUE
)

Arguments

result	result output from projectionDriveR function in PV mode
FC	fold change threshold, default at 0.2
pvalue	significance threshold, default set stored pvalue
subset	vector of gene names to subset the plot by
filter.inf	remove genes that have pvalues below machine double minimum value
label.num	Number of genes to label on either side of the volcano plot, default 5
display	boolean. Whether or not to plot and display volcano plots

Value

A list with weighted and unweighted differential expression metrics

genesofeve/projectR documentation built on June 12, 2025, 8:33 p.m.