WGCNA: overlapTable – R documentation

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overlapTable

Calculate overlap of modules

The function calculates overlap counts and Fisher exact test p-values for the given two sets of module assignments.

overlapTable(
    labels1, labels2, 
    na.rm = TRUE, ignore = NULL, 
    levels1 = NULL, levels2 = NULL)

`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`.

A list with the following components:

`countTable`	a 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.
`pTable`	a 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.

Peter Langfelder