plot_fdrtool: Make diagnostic plots for fdrtool results
In statOmics/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

plot_fdrtool

R Documentation

Make diagnostic plots for fdrtool results

Description

This function allows to make the three diagnostic plots from the fdrtool package by Korbinian Strimmer (http://strimmerlab.org) in separate windows. The implementation is identical to that in the fdrtool package, except that it allows to plot the functions separately. The first plot is also different in showing a histogram for both the vector of the observed test statistics x in white and a histogram for the subset of this vector that was used in the fdrtool_subset function in gray.

Usage

plot_fdrtool(result, make_plots = c(TRUE, TRUE, TRUE), color.figure = TRUE,
  verbose = TRUE)

Arguments

`result`	The result of a call to the `fdrtool_subset` function.
`make_plots`	A vector of three logical values. Each value indicates whether a certain plot should be made. Defaults to `c(TRUE, TRUE, TRUE)` indicating that all three plots should be made.
`color.figure`	A logical indicating whether a color figure or a black and white figure is produced. Defaults to `TRUE`, i.e. to color figure.
`verbose`	A logical indicating if status messages should be printed out. Defaults to `TRUE`.

Value

Diagnostic plots.

References

Strimmer, K. (2008a). A unified approach to false discovery rate estimation. BMC Bioinformatics 9: 303. Available from http://www.biomedcentral.com/1471-2105/9/303/.

Strimmer, K. (2008b). fdrtool: a versatile R package for estimating local and tail area- based false discovery rates. Bioinformatics 24: 1461-1462. Available from http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/12/1461.