Description Usage Arguments Value Citation References
View source: R/test_RV_target_module.R
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
1 2 3 | test_RV_target_module(OriginalData, Original_blockwiseModules,
target_module, X, permutations = 999, rarefied = FALSE,
reps_rarefaction = 1000, samplesize_rarefaction = NULL)
|
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) |
The function outputs a list with the following elements:
Observed RV coefficient
p value obtained through permutation
Results of the rarefaction analysis (empty if rarefied=FALSE)
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
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.