WGCNA: matchLabels – R documentation

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matchLabels

Relabel module labels to best match the given reference labels

Description

Given a source and reference vectors of module labels, the function produces a module labeling that is equivalent to source, but individual modules are re-labeled so that modules with significant overlap in source and reference have the same labels.

Usage

matchLabels(source, 
            reference, 
            pThreshold = 5e-2,
            na.rm = TRUE,
            ignoreLabels = if (is.numeric(reference)) 0 else "grey",
            extraLabels = if (is.numeric(reference)) c(1:1000) else standardColors()
            )

Arguments

`source`	a vector or a matrix of reference labels. The labels may be numeric or character.
`reference`	a vector of reference labels.
`pThreshold`	threshold of Fisher's exact test for considering modules to have a significant overlap.
`na.rm`	logical: should missing values in either `source` or `reference` be removed? If not, missing values may be treated as a standard label or the function may throw an error (exact behaviour depends on whether the input labels are numeric or not).
`ignoreLabels`	labels in `source` and `reference` to be considered unmatchable. These labels are excluded from the re-labeling procedure.
`extraLabels`	a vector of labels for modules in `source` that cannot be matched to any modules in `reference`. The user should ensure that this vector contains enough labels since the function automatically removes a values that occur in either `source`, `reference` or `ignoreLabels`, to avoid possible confusion.

Details

Each column of source is treated separately. Unlike in previous version of this function, source and reference labels can be any labels, not necessarily of the same type.

The function calculates the overlap of the source and reference modules using Fisher's exact test. It then attempts to relabel source modules such that each source module gets the label of the reference module that it overlaps most with, subject to not renaming two source modules to the same reference module. (If two source modules point to the same reference module, the one with the more significant overlap is chosen.)

Those source modules that cannot be matched to a reference module are labeled using those labels from extraLabels that do not occur in either of source, reference or ignoreLabels.

Value

A vector (if the input source labels are a vector) or a matrix (if the input source labels are a matrix) of the new labels.

Author(s)

Peter Langfelder