test_RV_target_module: Analysis of the association between a target module and one...

In fruciano/resampleWGCNA: Resampling-based analyses on WGCNA results

Description

Given a dataset, a set of results from blockwiseModules, a target module, and one or more variables, this function performs a permutation test based on Escoufier RV. Optionally, it can also compute rarefied estimates of RV. Notice that this function requires the package GeometricMorphometricsMix and that the analysis can be computationally demanding for large modules

Usage

test_RV_target_module(OriginalData, Original_blockwiseModules,
  target_module, X, permutations = 999, rarefied = FALSE,
  reps_rarefaction = 1000, samplesize_rarefaction = NULL)

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 association will be assessed
X	one or more variables whose association with the target module will be tested
permutations	number of permutations to use in the test of association
rarefied	if TRUE, it also performs rarefaction-based estimation of Escoufier RV
reps_rarefaction	number of replicated rarefied samples
samplesize_rarefaction	sample size to which rarefy (required if rarefied=TRUE)

Value

The function outputs a list with the following elements:

ObsRV

Observed RV coefficient

p_value_perm

p value obtained through permutation

Rarefied_RV

Results of the rarefaction analysis (empty if rarefied=FALSE)

Citation

If you use this function please cite Fruciano et al. 2019 (development of the method for WGCNA results) and Escoufier 1973 (for the use of the RV statistic).

If you use the option to get rarefied estimates, in addition to the above, please kindly cite Fruciano et al. 2013

References

Escoufier Y. 1973. Le Traitement des Variables Vectorielles. Biometrics 29:751-760.

Fruciano C., Franchini P., Meyer A. 2013. Resampling-Based Approaches to Study Variation in Morphological Modularity. PLoS ONE 8:e69376.

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.