getModulePreservation: Determine module preservation between reference and query...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Determine module preservation between reference and query network

Description

Determine module preservation between reference and query network using expression matrices from two scRNAseq comparison groups. Uses WGCNA::modulePreservation() to assess how well a module in one sample is preserved in another. 5<Z<10 indicates moderate presevation, while Z>10 indicates high preservation. Grey module contains uncharacterized genes while gold module contains random genes (these are used as controls). Note that future updates will extend the functionality to accomodate >2 networks.

Usage

getModulePreservation(
  ref.mat,
  query.mat,
  ref.module,
  query.modules = NULL,
  networkType = "unsigned",
  referenceNetworks = 1,
  ...
)

Arguments

ref.mat	reference data (expression matrix, cols are genes and rows and samples)
query.mat	query data (expression matrix, cols are genes and rows and samples)
query.modules	query module membership. Vector of colors (length is equal to number of samples), specfiying sample membership to each module.
networkType	Allowed values are (unique abbreviations of) "unsigned", "signed", "signed hybrid". See WGCNA::adjacency.
referenceNetworks	a vector giving the indices of expression data to be used as reference networks. Reference networks must have their module labels given in multiColor.
...	Additional arguments passessed to modulePreservation WGCNA package
ref.modules	reference module membership. Vector of colors (length is equal to number of samples), specfiying sample membership to each module.

Value

data.frame of module preservation statistics

See Also

modulePreservation

Examples

mColorh.1 <- optimalDS(dist2hclust(d.1), d.1, pamStage = F,cutHeight = 0.99)
modules.1 = mColorh.1[,4]

stats <- getModulePreservation(ref.mat = de.1, query.mat = de.2, modules.1, nPermutations=30,maxGoldModuleSize=100,maxModuleSize=400, verbose=3)

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.