volcanoPlot.numeric: Volcano plot

In pneuvial/sanssouci: Post Hoc Multiple Testing Inference

Volcano plot

Description

Volcano plot for differential expression studies

Usage

## S3 method for class 'numeric'
volcanoPlot(
  x,
  y,
  pval,
  thr,
  p = 1,
  q = 1,
  r = 0,
  cex = c(0.2, 0.6),
  col = c("#33333333", "#FF0000", "#FF666633"),
  pch = 19,
  ylim = NULL,
  bounds = TRUE,
  ...
)

Arguments

x	A vector of fold changes (x axis of the volcano plot)
y	A vector of p-values (y axis of the volcano plot)
pval	A vector of p-values, of the same length as x, use to estimate post-hoc bounds
thr	A numeric vector of length K, a JER controlling family, used to estimate post-hoc bounds
p	A numeric value, the p-value threshold under which genes are selected
q	A numeric value, the q-value (or FDR-adjusted p-value) threshold under which genes are selected
r	A numeric value, the absolute fold change above which genes are selected
cex	A numeric vector of length 2, the relative magnification factor for unselected (cex[1]) and unselected (cex[2]) genes.
col	A vector of length 3
pch	An integer or single character string specifying the plotting character, see par
ylim	A numeric vector of length 2, the y limits of the plot
bounds	A boolean value: should the post hoc bounds be displayed on the plot? Defaults to TRUE
...	Not used

Details

A Welch T-test of differential expression between the two categories defined by categ are applied for each gene using the rowWelchTests function, which also outputs the "fold change" (mean difference in log scale) between the two categories.

Value

The indices of selected genes (returned invisibly)

See Also

Volcano plot shiny app at https://shiny-iidea-sanssouci.apps.math.cnrs.fr/

pneuvial/sanssouci documentation built on Feb. 12, 2024, 4:18 a.m.