Full FUSE segmentation pipeline

Performs the full FUSE segmentation workflow: hierarchical clustering, model selection, tree cutting, and genomic segment summarization.

Usage

fuse.segment(x, ...)

# Default S3 method
fuse.segment(x, K1, chr, pos, method = c("BIC", "AIC"), ...)

# S3 method for class 'BSseq'
fuse.segment(x, method = c("BIC", "AIC"), ...)

# S3 method for class 'methrix'
fuse.segment(x, method = c("BIC", "AIC"), ...)

Arguments

x

Input object. One of:

matrix

Unmethylated count matrix (K0).

BSseq

A BSseq object.

methrix

A methrix object.

...

Additional arguments (matrix input only)

K1

Methylated count matrix (if x is matrix).

chr

Chromosome labels (if x is matrix).

pos

Genomic positions (if x is matrix.

method

Information criterion for model selection: "BIC" (default) or "AIC".

For internal use, x corresponds to the unmethylated count matrix (K0).

Value

An object of class fuse_summary, containing:

summary

Data frame with one row per genomic segment.

betas_per_segment

Matrix of per-sample methylation estimates.

raw_beta

Per-CpG methylation estimates.

raw_pos

Genomic positions of CpGs.

Details

fuse.segment() is an S3 generic with methods for:

matrix

Raw count matrices (K0, K1) with genomic annotation.

BSseq

Bioconductor BSseq objects.

methrix

Bioconductor methrix objects (supports DelayedMatrix).

Automatic data extraction

For BSseq objects:

• Methylated counts are obtained via getCoverage(x, "M")

• Unmethylated counts via getCoverage(x, "Cov") - M

• Chromosome and position from rowRanges(x)

For methrix objects:

• Methylated counts via get_matrix(x, "M")

• Total coverage via get_matrix(x, "C")

• Unmethylated counts computed as C - M

• Genomic coordinates extracted from locus metadata