runWGCNA: run WGCNA analysis on scRNAseq expression matrix

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

run WGCNA analysis on scRNAseq expression matrix

Description

Run WGCNA analysis on scRNAseq expression matrix, using WGCNA R package.

Usage

runWGCNA(
  e.mat,
  s.mat = NULL,
  cor.metric = "rho_p",
  soft.power = 2,
  use.TOM = T,
  network.type = "signed",
  TOM.type = "unsigned",
  rescale.adjacency = F,
  verbose = T,
  ...
)

Arguments

e.mat	Expression matrix. Row entries are cells, column entries are genes. Colnames and rownames are expected.
s.mat	Similarity matrix (optional). If not provided, will be computed using method specfiied by cor.metric. If provided, s.mat is not recomputed.
cor.metric	Correction measure to use. Default is "rho_p". See "dismay" package for additional options.
soft.power	Soft power used to scale s.mat to a.mat (e.g., a.mat = s.mat ^ soft.power)
use.TOM	Logical flag specifying whether to compute topoligical overlap matrix. If false, w.mat = a.mat.
network.type	Network type. Allowed values are (unique abbreviations of) "unsigned", "signed" (default), "signed hybrid"
TOM.type	TOM type. Allowed values are "unsigned" (default) or "signed"
rescale.adjacency	Logical indicate whether adjacency matrix is rescaled to [0,1]. Default is False.
verbose	Print progress. Default is TRUE
...	Additional arguments passessed to TOMsimilarity WGCNA package

Value

List containing similarity matrix (s.mat), adacency matrix (a.mat), topological overlap matrix (w.mat) and disimilarity matrix (d.mat)

Examples

# Get expression matrix
which.data <- "scale"

# variable gene only matrix
use.var <- T
if (use.var){
  exp.mat <- getExpressionMatrix(so.query, only.variable = use.var, which.data = which.data, use.additional.genes = NA)
} else {
  exp.mat <- exp.mat.complete
}


# transpose expressio matrix (genes are columns)
t.exp.mat <- t(exp.mat)
datExpr <- as.matrix(t.exp.mat)
SubGeneNames=colnames(datExpr)

# capture output used to hide undesired print statement
print2hide <- capture.output(allowWGCNAThreads())

# transform matrix if necessary
if (min(datExpr) < 0) {
  datExpr.noz <- datExpr + abs(min(datExpr))
} else {
  datExpr.noz <- datExpr
}

# run WGCNA
output.all <- runWGCNA(datExpr.noz, cor.metric = "rho_p", soft.power = 2, use.TOM = T)

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