volcanoplot-methods: Make a volcano plot of the outcome of a uWMW test

In CenterForStatistics-UGent/unifiedWMWqPCR: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Make a volcano plot of the outcome of a uWMW test

Description

This function creates a volcano plot of the outcome of a uWMW test. In this plot, the p-value is plotted against the odd ratio or the log-odds ratio, depending on what interests you most. It allows to quickly see what proportion of results is significant, and what proportion of significant results has a biologically significant chance of being upregulated.

Usage

## S4 method for signature 'uwmwRes'
volcanoplot(
  fit,
  esttype = c("logor", "or", "logodds", "odds", "p"),
  transf.y = function(i) -log10(i),
  ref.y = -log10(0.05),
  ...
)

## S4 method for signature 'matrix'
volcanoplot(fit, ...)

## S4 method for signature 'numeric'
volcanoplot(fit, ...)

## S4 method for signature 'MArrayLM'
volcanoplot(fit, coef = 1, highlight = 0, ...)

Arguments

fit	a uwmwRes object, a matrix with 2 columns or a numeric vector with either odds ratios or the log of odds ratios.
esttype	The estimate that should be plotted from the uwmwRes object. See also getEstimate.
transf.y	a function used to transpose the values on the Y axis. For uwmwRes objects, defaults to -log10(y). Passed down to internal function.
ref.y	The location on the Y axis for the reference line.
...	arguments passed to the internal function. See volcanopar
coef	for compatibility with limma package, see volcanopar
highlight	for compatibiity with limma package, see volcanopar

Details

The methods described here all use the same internal function to create the plot

Value

invisible NULL

Author(s)

Joris Meys

Examples

data(NBmat)
housekeeping.id <- grep("let",rownames(NBmat),value=TRUE)
NB.Htest <- uWMW(NBmat,NBgroups,housekeeping.id)

volcanoplot(NB.Htest)
volcanoplot(NB.Htest,"p")

CenterForStatistics-UGent/unifiedWMWqPCR documentation built on Oct. 28, 2024, 2:34 p.m.