getModules: Identify Modules of Comethylated Regions

In cemordaunt/comethyl: An R Package for Weighted Region Comethylation Network Analysis

Identify Modules of Comethylated Regions

Description

getModules() builds a comethylation network, identifies comethylated modules, outputs a list with region module assignments, eigennode values, dendrograms, and module membership, and then saves this as a .rds file.

Usage

getModules(
  meth,
  power,
  regions,
  maxBlockSize = 40000,
  corType = c("pearson", "bicor"),
  maxPOutliers = 0.1,
  deepSplit = 4,
  minModuleSize = 10,
  mergeCutHeight = 0.1,
  nThreads = 4,
  save = TRUE,
  file = "Modules.rds",
  verbose = TRUE
)

Arguments

meth	A numeric matrix, where each row is a sample and each column is a region. This is typically obtained from adjustRegionMeth().
power	A numeric(1) giving the soft-thresholding power. This is typically obtained from getSoftPower().
regions	A data.frame of regions, typically after filtering with filterRegions(). Must have the column RegionID and correspond to the regions in meth.
maxBlockSize	A numeric(1) specifying the maximum number of regions in a block. If there are more than this number regions, then regions are pre-clustered into blocks using projective K-means clustering. Decrease this if memory is insufficient.
corType	A character(1) indicating which correlation statistic to use in the adjacency calculation.
maxPOutliers	A numeric(1) specifying the maximum percentile that can be considered outliers on each side of the median for the bicor statistic.
deepSplit	A numeric(1) specifying the sensitivity for module detection. Possible values are integers 0 to 4, with 4 having the highest sensitivity.
minModuleSize	A numeric(1) giving the minimum number of regions to qualify as a module.
mergeCutHeight	A numeric(1) specifying the cut height for merging correlated modules. Value is the maximum dissimilarity (1 - correlation) and ranges from 0 to 1.
nThreads	A numeric(1) indicating the number of threads for correlation calculations.
save	A logical(1) indicating whether to save the list.
file	A character(1) giving the file name (.rds) for the saved list.
verbose	A logical(1) indicating whether messages should be printed.

Details

Comethylation networks are built and modules are identified by WGCNA::blockwiseModules(), with corType set to either pearson or bicor. Calculations are performed for a signed network in blocks of regions of maximum size maxBlockSize (default = 40000). If there are more than maxBlocksize regions, then regions are pre-clustered into blocks using projective K-means clustering. Region correlations are performed within each block and regions are clustered with average linkage hierarchical clustering. Modules are then identified with a dynamic hybrid tree cut and highly correlated modules are merged together. More information is given in the documentation for WGCNA::blockwiseModules().

Value

A list with 11 elements. See WGCNA::blockwiseModules() for a description of these. Additional regions element is a data.frame with the region locations, statistics, module assignment, module membership, and hub region status.

See Also

• getRegionMeth(), getPCs(), and adjustRegionMeth() to extract methylation data and then adjust it for the top principal components.

• getSoftPower() and plotSoftPower() to estimate the best soft-thresholding power and visualize scale-free topology fit and connectivity.

• plotRegionDendro() and getModuleBED() to visualize region similarity, genomic locations, and module assignments.

Examples

## Not run: 

# Get Methylation Data
meth <- getRegionMeth(regions, bs = bs, file = "Region_Methylation.rds")

# Adjust Methylation Data for PCs
mod <- model.matrix(~1, data = pData(bs))
PCs <- getPCs(meth, mod = mod, file = "Top_Principal_Components.rds")
methAdj <- adjustRegionMeth(meth, PCs = PCs,
                            file = "Adjusted_Region_Methylation.rds")

# Select Soft Power Threshold
sft <- getSoftPower(methAdj, corType = "pearson", file = "Soft_Power.rds")
plotSoftPower(sft, file = "Soft_Power_Plots.pdf")

# Get Comethylation Modules
modules <- getModules(methAdj, power = sft$powerEstimate, regions = regions,
                      corType = "pearson", file = "Modules.rds")

# Visualize Comethylation Modules
plotRegionDendro(modules, file = "Region_Dendrograms.pdf")
BED <- getModuleBED(modules$regions, file = "Modules.bed")

## End(Not run)

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.