Description Usage Arguments Details Value Author(s) See Also

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.

1 2 3 4 5 6 7 | ```
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()
)
``` |

`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 |

`ignoreLabels` |
labels in |

`extraLabels` |
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 `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`

.

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.

Peter Langfelder

`overlapTable`

for calculation of overlap counts and p-values;

`standardColors`

for standard non-numeric WGCNA labels.

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