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
reference have the same labels.
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() )
a vector or a matrix of reference labels. The labels may be numeric or character.
a vector of reference labels.
threshold of Fisher's exact test for considering modules to have a significant overlap.
logical: should missing values in either
a vector of labels for modules in
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
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
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.)
source modules that cannot be matched to a
reference module are labeled using
those labels from
extraLabels that do not occur in either of
A vector (if the input
source labels are a vector) or a matrix (if the input
labels are a matrix) of the new labels.
overlapTable for calculation of overlap counts and p-values;
standardColors for standard non-numeric WGCNA labels.
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