test_eigengene_explained_variance: Test the significance of a target eigengene

Description Usage Arguments Details Value Citation References

View source: R/test_eigengene_explained_variance.R

Description

Performs a permutation test of significance for the eigengene

Usage

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test_eigengene_explained_variance(OriginalData, Original_blockwiseModules,
  target_module, permutations = 999, usebicor = FALSE, ...)

Arguments

OriginalData

Matrix or data frame containing the original data on which the blockwiseModules function has been run (observations in rows, variables in columns).

Original_blockwiseModules

output of the blockwiseModules function

target_module

module whose largest eigenvalue/eigengene will be tested

permutations

number of permutations to use

usebicor

whether one should use the standard eigengene function in WGCNA (default), or bicor

...

further parameters to be passed to either moduleEigengenes or bicor

Details

Given a dataset, a set of results from blockwiseModules, and a target module, this function performs a permutation test of the variance explained by the eigengene (first eigenvalue of the correlation matrix of the genes belonging to the module). The target module should be expressed in the same way as when using blockwiseModules (i.e., color or number) Notice that option bicor=TRUE can be extremely computationally demanding

Value

The function outputs a list with the following elements:

moduleEigengenes_ALL

The eigengenes for all the modules (will be empty if bicor=TRUE)

explained_variance_target_module

The observed explained variance for the target module

p_value

The p value obtained through permutation

Citation

If you use this function please cite Fruciano et al. 2019

References

Fruciano, C., Meyer, A., Franchini, P. 2019. Divergent allometric trajectories in gene expression and coexpression produce species differences in sympatrically speciating Midas cichlid fish. Genome Biology and Evolution 11, 1644-1657.


fruciano/resampleWGCNA documentation built on Feb. 11, 2022, 5:38 a.m.