summary.fdr.result: Display functions for local fdr output
Description
Display functions for output from fdr1d and fdr2d, summarizing the output, displaying the proportion of non-differentially expressed genes and extracting the list of top-regulated genes.
Usage
summary.fdr.result(object, ...)
p0(x, how = FALSE)
topDE(x, co = 0.1)
Arguments
x, object
an object of class fdr.result created by fdr1d or fdr2d.
how
a logical value indicating whether to return only the numerical value of the proportion of non-differentially expressed genes, or a list whose second element indicates whether the proportion was estimated from the data or supplied by the user.
...
extra arguments, currently unused
co
cutoff for either FDR or fdr
Value
For summary.fdr.result, a list with the summary items.For p0, either a numerical value or a list with two elements, depending on the value of parameter how.For topDE, the genes that have FDR (EOC) or fdr (fdr1d, fdr2d) less or equal than co, sorted by FDR or fdr respectively.