overlapTable: Calculate overlap of modules
Description
The function calculates overlap counts and Fisher exact test p-values for the given two sets of module
assignments.Usage
overlapTable(
labels1, labels2,
na.rm = TRUE, ignore = NULL,
levels1 = NULL, levels2 = NULL)Arguments
labels1
a vector containing module labels.
labels2
a vector containing module labels to be compared to labels1.
na.rm
logical: should entries missing in either labels1 or labels2 be removed?
ignore
an optional vector giving label levels that are to be ignored.
levels1
optional vector giving levels for labels1. Defaults to sorted unique non-missing
values in labels1 that are not present in ignore.
levels2
optional vector giving levels for labels2. Defaults to sorted unique non-missing
values in labels2 that are not present in ignore.
Value
- A list with the following components:
- countTablea matrix whose rows correspond to modules (unique labels) in
labels1 and whose
columns correspond to modules (unique labels) in labels2, giving the number of objects in the
intersection of the two respective modules. - pTablea matrix whose rows correspond to modules (unique labels) in
labels1 and whose
columns correspond to modules (unique labels) in labels2, giving Fisher's exact test
significance p-values for the overlap of the two respective modules.