gintervals.to_mat: Convert intervals + values data.frame to an interval-indexed...

In misha: Toolkit for Analysis of Genomic Data

Convert intervals + values data.frame to an interval-indexed matrix

Description

Builds a numeric matrix of value columns whose rows are indexed by intervals. The intervals are carried in attr(mat, "intervals") as the authoritative identity; rownames(mat) are display-only (default "chrom:start-end") and are NEVER parsed back by gintervals.from_mat. This avoids the round-trip corruption that occurs when chrom names contain underscores or other separators.

Usage

gintervals.to_mat(df, id_col = NULL, value_cols = NULL, labels = TRUE)

Arguments

df	data.frame with chrom, start, end and zero or more value columns. May contain an intervalID column (from gextract), which is kept in the attribute but excluded from the matrix.
id_col	optional column name in df whose values become rownames. If NULL (default), rownames are "chrom:start-end".
value_cols	character vector of column names to use as matrix data. If NULL (default), auto-detect: all columns except chrom, start, end, intervalID. Auto-detect errors if any selected column is non-numeric; pass value_cols explicitly to override.
labels	if TRUE (default), set rownames(mat) to either df[[id_col]] (if id_col is supplied) or "chrom:start-end". If FALSE, leave rownames NULL - useful in pipelines that don't need the display labels and would prefer to skip the construction cost on large inputs. When FALSE, the id_col argument is ignored.

Value

An intervs_mat object: a numeric matrix subclass with the intervals attached as attr(., "intervals"). Supports row/column subsetting ([) and rbind() while preserving the attribute.

See Also

gintervals.from_mat

Examples

df <- data.frame(
    chrom = c("chr1", "chr1", "chr2"),
    start = c(100L, 500L, 200L),
    end   = c(200L, 700L, 400L),
    t1    = c(1.5, 2.5, 3.5),
    t2    = c(10, 20, 30)
)
mat <- gintervals.to_mat(df)
rownames(mat)
# subset preserves intervals:
sub <- mat[c(1, 3), ]
attr(sub, "intervals")
# round-trip back to a data.frame:
gintervals.from_mat(sub)

misha documentation built on Aug. 24, 2026, 5:14 p.m.