Visualizes how DMR blocks are formed on a single chromosome by layering raw scores, smoothed scores, piecewise-linear segments, slope-based candidate blocks, distance-based split boundaries, and final accepted blocks.
Usage
plotDMRBlockFormation(
dmrs,
chromosome,
genome = "hg38",
k_neighbors = 5L,
min_segment_size = 2L,
block_gap_mode = "adaptive",
block_gap_fixed_bp = NULL,
block_gap_quantile = 0.95,
block_gap_multiplier = 1.5,
block_gap_min_bp = 250000,
block_gap_max_bp = 5e+06,
point_alpha = 0.7,
point_size = 1
)Arguments
- dmrs
GRanges object or data frame. DMR results from
buildDMRsorscoreDMRs.- chromosome
Character. Chromosome to inspect (e.g.,
"chr7"or"7").- genome
Character. Genome version passed to
.convertToGRanges(default:"hg38").- k_neighbors
Integer. Number of nearest neighbors used in adaptive Gaussian smoothing (default:
5).- min_segment_size
Integer. Minimum size of linear segments in PELT segmentation (default:
2).- block_gap_mode
Character. Gap rule for block splitting:
"adaptive"(default),"fixed", or"none".- block_gap_fixed_bp
Numeric. Maximum allowed midpoint gap (bp) when
block_gap_mode = "fixed". Ignored otherwise.- block_gap_quantile
Numeric in
(0, 1). Gap quantile used for adaptive thresholding (default:0.95).- block_gap_multiplier
Numeric > 0. Multiplier for adaptive gap threshold (default:
1.5).- block_gap_min_bp
Numeric >= 0. Lower clamp for adaptive gap threshold (bp). Default is
250000.- block_gap_max_bp
Numeric >=
block_gap_min_bp. Upper clamp for adaptive gap threshold (bp). Default is5000000.- point_alpha
Numeric. Alpha for raw score points in
[0, 1](default:0.7).- point_size
Numeric. Point size for raw scores (default:
1.0).
Examples
dmrs <- data.frame(
chr = "chr7",
start = seq(1e6, by = 5e4, length.out = 10),
end = seq(1e6, by = 5e4, length.out = 10) + 100,
score = seq(0.5, 0.8, length.out = 10)
)
p <- plotDMRBlockFormation(dmrs, chromosome = "chr7")