gsynth.bin_map: Create a bin mapping from value-based merge specifications

In misha: Toolkit for Analysis of Genomic Data

Create a bin mapping from value-based merge specifications

Description

Converts value-based bin merge specifications into a bin_map named vector that can be used with gsynth.train. This allows you to specify merges using actual track values rather than bin indices.

Usage

gsynth.bin_map(breaks, merge_ranges = NULL)

Arguments

breaks	Numeric vector of bin boundaries (same as used in gsynth.train)
merge_ranges	List of merge specifications. Each specification is a named list with: from Numeric vector of length 2 c(min, max) defining the source value range to merge. Use -Inf or Inf for open-ended ranges. Can also be a single number (shorthand for c(value, Inf)). to Numeric vector of length 2 c(min, max) defining the target bin that source bins should map to. Must match an existing bin defined by breaks.

Value

A named vector (bin_map) compatible with bin_map parameter in gsynth.train. The names are source bin indices (1-based), and values are target bin indices (1-based).

See Also

gsynth.train

Examples

# Define breaks for GC content [0, 1] in 0.025 increments
breaks <- seq(0, 1, 0.025)

# Merge all GC content above 70% (0.7) into the bin (0.675, 0.7]
bin_map <- gsynth.bin_map(
    breaks = breaks,
    merge_ranges = list(
        list(from = 0.7, to = c(0.675, 0.7))
    )
)

# Multiple merges: merge low GC (< 0.3) and high GC (> 0.7) into middle bins
bin_map2 <- gsynth.bin_map(
    breaks = breaks,
    merge_ranges = list(
        list(from = c(-Inf, 0.3), to = c(0.4, 0.425)), # low GC -> (0.4, 0.425]
        list(from = 0.7, to = c(0.675, 0.7)) # high GC -> (0.675, 0.7]
    )
)

misha documentation built on Jan. 28, 2026, 1:07 a.m.