Example Genomic Ranges for Documentation, Tests, and Tutorials

fast_ranges_example is a small reproducible dataset shipped with the package. It is intended for documentation examples, teaching, unit tests, and quick smoke checks of overlap workflows.

Format

A named list with two components:

query: A GRanges object with 6 genomic intervals and metadata columns query_id and score.
subject: A GRanges object with 7 genomic intervals and metadata columns gene_id and biotype.

Source

Generated from data-raw/make_example_data.R, which also writes matching BED files to inst/extdata/.

Details

The object is a named list with two GRanges components:

query: six example genomic intervals that behave like user-supplied peaks, windows, or regions of interest.
subject: seven example genomic intervals that behave like annotation features such as genes, promoters, enhancers, or other reference ranges.

Metadata columns are included so examples can demonstrate joins, grouped summaries, and overlap aggregation:

query contains query_id and score
subject contains gene_id and biotype

The same records are also distributed as plain BED files in inst/extdata/query_peaks.bed and inst/extdata/subject_genes.bed. Use the in-memory dataset when you want a ready-to-run example in R, and use the BED files when you want to demonstrate file import or command-line workflows.

This dataset is intentionally small and synthetic. It is designed for examples and tests, not as a biological reference resource.

Examples

data("fast_ranges_example", package = "fastRanges")
query <- fast_ranges_example$query
subject <- fast_ranges_example$subject

query
#> GRanges object with 6 ranges and 2 metadata columns:
#>       seqnames    ranges strand |    query_id     score
#>          <Rle> <IRanges>  <Rle> | <character> <integer>
#>   [1]     chr1   100-159      + |          q1         8
#>   [2]     chr1   180-269      + |          q2        10
#>   [3]     chr1   350-419      - |          q3         6
#>   [4]     chr2     40-79      * |          q4         3
#>   [5]     chr2   300-379      + |          q5         9
#>   [6]     chr3     10-34      - |          q6         5
#>   -------
#>   seqinfo: 3 sequences from an unspecified genome; no seqlengths
subject
#> GRanges object with 7 ranges and 2 metadata columns:
#>       seqnames    ranges strand |     gene_id     biotype
#>          <Rle> <IRanges>  <Rle> | <character> <character>
#>   [1]     chr1    90-169      + |          gA    promoter
#>   [2]     chr1   210-309      - |          gB    enhancer
#>   [3]     chr1   320-369      - |          gC    enhancer
#>   [4]     chr2     20-89      + |          gD    promoter
#>   [5]     chr2   330-419      * |          gE   gene_body
#>   [6]     chr3      1-40      - |          gF    promoter
#>   [7]     chr3    80-114      + |          gG    enhancer
#>   -------
#>   seqinfo: 3 sequences from an unspecified genome; no seqlengths

fast_find_overlaps(query, subject, threads = 1)
#> Hits object with 5 hits and 0 metadata columns:
#>            from        to
#>       <integer> <integer>
#>   [1]         1         1
#>   [2]         3         3
#>   [3]         4         4
#>   [4]         5         5
#>   [5]         6         6
#>   -------
#>   nLnode: 6 / nRnode: 7