Summarize FUSE Segmentation Results

Summarizes FUSE segmentation results into one row per segment, including genomic coordinates, CpG count, segment length, average methylation (beta), and stability flag based on likelihood testing. Also returns per-sample methylation estimates for each segment. Result can be visualized using plot(result).

Usage

fuse.summary(K0, K1, chr, pos, segments)

Arguments

K0

Integer or numeric matrix of unmethylated counts.

K1

Integer or numeric matrix of methylated counts.

chr

Character vector giving the chromosome for each site.

pos

Numeric vector giving genomic coordinates for each site.

segments

Integer vector giving segment IDs for each site in K0 and K1.

Value

A list with four elements:

summary

A data frame with one row per segment and the following columns:

Segment: Segment ID Chr: Chromosome Start: Start genomic coordinate End: End genomic coordinate CpGs: Number of CpGs in the segment Length: Genomic length (End - Start + 1) Beta: Average methylation across samples and CpGs Coherent: Logical indicator (TRUE if segment is coherently methylated, else FALSE)

betas_per_segment

Matrix of per-sample methylation estimates for each segment (rows = segments, columns = samples).

raw_beta

Average beta per CpG site, used for plotting.

raw_pos

Genomic position for every given CpG site, used for plotting.

Examples

set.seed(1234)
K0 <- matrix(
  rep(c(sample(0:20, 200, replace = TRUE), sample(20:40, 200, replace = TRUE)), 2),
  nrow = 100, byrow = TRUE
)
K1 <- matrix(
  rep(c(sample(20:40, 200, replace = TRUE), sample(0:20, 200, replace = TRUE)), 2),
  nrow = 100, byrow = TRUE
)
tree <- fuse.cluster(K0, K1)
segments <- fuse.cut.tree(tree, 4)
res <- fuse.summary(K0, K1, rep("chr1", nrow(K0)), 1:nrow(K0), segments)
head(res$summary)
#>   Segment  Chr Start End CpGs Length      Beta Coherent
#> 1  chr1.1 chr1     1  25   25     25 0.7523929    FALSE
#> 2 chr1.26 chr1    26  50   25     25 0.2355517    FALSE
#> 3 chr1.51 chr1    51  75   25     25 0.7523929    FALSE
#> 4 chr1.76 chr1    76 100   25     25 0.2355517    FALSE
head(res$betas_per_segment)
#>              [,1]      [,2]      [,3]      [,4]      [,5]      [,6]      [,7]
#> chr1.1  0.7895277 0.7677083 0.7163462 0.7583893 0.7068311 0.7875920 0.7548919
#> chr1.26 0.2435233 0.2213667 0.2137791 0.2308478 0.2693467 0.2171665 0.2216700
#> chr1.51 0.7895277 0.7677083 0.7163462 0.7583893 0.7068311 0.7875920 0.7548919
#> chr1.76 0.2435233 0.2213667 0.2137791 0.2308478 0.2693467 0.2171665 0.2216700
#>              [,8]
#> chr1.1  0.7444562
#> chr1.26 0.2651515
#> chr1.51 0.7444562
#> chr1.76 0.2651515