summary.fdr.result {OCplus} | R Documentation |
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.
summary.fdr.result(object, ...) p0(x, how = FALSE) topDE(x, co = 0.1)
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 |
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.
A. Ploner
# Create object res1d example(fdr1d) summary(res1d) p0(res1d) p0(res1d, how=TRUE) topDE(res1d)