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methFuse

methFuse implements FUSE: FUnctional SEgmentation of DNA methylation data through hierarchical clustering.

Features

• Hierarchical clustering based on methylation count matrices
• Detection of optimal number of clusters
• Summarization of segments, including stability flag
• Per-segment methylation estimates per sample

Installation

From GitHub (Development Version)

Either using remotes: (recommended)

# Install remotes if needed
install.packages("remotes")

# Install fuseR from GitHub
remotes::install_github("holmsusa/methFuse")

or using devtools:

# Install devtools if needed
install.packages("devtools")

# Install fuseR from GitHub
devtools::install_github("holmsusa/methFuse")

System Requirements

• R version ≥ 4.0
• C++ toolchain for native code compilation

You may need platform-specific tools:

• macOS: Xcode Command Line Tools (xcode-select –install)
• Linux: build-essential
• Windows: Rtools

Supported input types

fuse.segment() supports the following input formats:

• Matrix input
  • Unmethylated counts (K0)
  • Methylated counts (K1)
  • Explicit chromosome (chr) and position (pos) vectors
• BSseq objects (Bioconductor)
  • Counts and genomic coordinates are extracted automatically
  • Requires bsseq package
• methrix objects (Bioconductor)
  • Supports large datasets via DelayedMatrix
  • Counts and genomic coordinates are extracted automatically
  • Requires methrix and DelayedArray packages

Install needed packages with

BiocManager::install(c("bsseq", "methrix", "DelayedArray"))

Quick Example

library(fuseR)
set.seed(1234)

# Generate sample data
# Unmethylated counts, T's
K0 <- matrix(
  rep(c(sample(0:20, 200, replace = TRUE), sample(20:40, 200, replace = TRUE)), 2),
  nrow = 100, byrow = TRUE
)
# Methylated counts, C's
K1 <- matrix(
  rep(c(sample(20:40, 200, replace = TRUE), sample(0:20, 200, replace = TRUE)), 2),
  nrow = 100, byrow = TRUE
)

# Perform segmentation
segment_result <- fuse.segment(
  K0, K1, 
  chr = sub("\\..*$", "", rownames(K0)), 
  pos = as.numeric(sub("^.*\\.", "", rownames(K0)))
)

# Access summary and per-segment betas
head(segment_result$summary)
head(segment_result$betas_per_segment)

Check out a full example workflow in the vignette.

License

This package is licensed under the MIT License. See LICENSE for details.

Author

Susanna Holmstrom

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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