Find features overlapping a genomic region — region-queries • lkparq

Efficient region queries that use chromosome-based filtering before computing overlaps.

Usage

genes_in_region(x, region, ...)

transcripts_in_region(x, region, ...)

Arguments

x: A GTFParquet object.
region: A GRanges object specifying the query region(s).
...: Additional arguments passed to genes() or transcripts().

Value

A GRanges object containing features that overlap the query region.

Details

These functions first filter by chromosome (using Parquet predicate pushdown for efficiency), then compute overlaps using findOverlaps.

Examples

if (FALSE) { # \dontrun{
gtf <- GTFParquet(system.file("gc49", package="lkparq"))

# Define a query region
region <- GRanges("chr1", IRanges(1000000, 2000000))

# Find overlapping genes
genes_in_region(gtf, region)

# Find overlapping transcripts (protein-coding only)
transcripts_in_region(gtf, region, 
                      filter = list(transcript_type = "protein_coding"))
} # }