Description Usage Arguments Details Value Author(s) Examples
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.
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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, ...)
|
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 |
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 |
coef |
for compatibility with limma package, see |
highlight |
for compatibiity with limma package, see |
The methods described here all use the same internal function to create the plot
invisible NULL
Joris Meys
1 2 3 4 5 6 |
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