IGD in R (gtars)

Low-level R bindings for IGD (Indexed Genomic Data) — a fast binary index over collections of BED files, used internally by gtars LOLA and by the BEDbase retrieval pipeline. The R API exposes two functions: igd_create (build an index from BED files on disk) and igd_search (query an existing index with a BED file).

If you're running LOLA enrichment, you usually don't need to touch IGD directly — loadRegionDB() in r/lola.md builds an IGD index internally from the region database. Use this page if you want to index a custom collection of BED files and query it directly.

Creating an IGD database

library(gtars)

igd_create(
  output_path = "path/to/output/",
  filelist    = "path/to/bed/files/",
  db_name     = "igd_database",  # default
)

Arguments:

output_path — directory where the IGD database files will be written. Created if it does not exist.
filelist — one of:
- a path to a .txt file listing BED file paths (one per line; the .txt extension is how it is recognized),
- a path to a directory containing BED files (all .bed and .gz files in it are indexed),
- "-" or "stdin" to read paths from standard input.
db_name — prefix for the output filenames (default "igd_database"). The function produces two files: <db_name>.igd (the index) and <db_name>.tsv (file metadata).

Returns NULL invisibly on success. Errors are raised via stop() on invalid input.

Example

# From a directory of BED files
igd_create(
  output_path = "./igd_out",
  filelist    = "./my_bed_files/",
  db_name     = "my_peaks",
)

# Produces:
# ./igd_out/my_peaks.igd
# ./igd_out/my_peaks.tsv

# From an explicit file list
writeLines(
  c("./rep1.bed", "./rep2.bed", "./rep3.bed"),
  "bed_list.txt",
)
igd_create(
  output_path = "./igd_out",
  filelist    = "bed_list.txt",
  db_name     = "replicates",
)

Searching an IGD database

hits <- igd_search(
  database_path = "path/to/my_peaks.igd",
  query_path    = "path/to/query.bed",
)

Arguments:

database_path — path to an existing .igd file (produced by igd_create or any other IGD-compatible tool).
query_path — path to a BED file containing the query regions.

Returns a data.frame with one row per database file that has at least one hit, and columns filename, numRegions (regions in that file), and hits (number of overlaps with the query).

Example

hits <- igd_search(
  database_path = "./igd_out/my_peaks.igd",
  query_path    = "query.bed",
)

head(hits)

# Typical analysis: rank database files by overlap count
hits[order(-hits$hits), ]

Relationship to other gtars R functions

loadRegionDB() in lola.R — builds an IGD index internally for a LOLA region database. The IGD is wrapped inside a RegionDB pointer and used by runLOLA(). Users running enrichment typically don't need to call igd_create / igd_search separately.
countOverlaps() / findOverlaps() on RegionSet — ad-hoc overlap queries between two RegionSet objects use the AIList index from gtars-overlaprs, not IGD. Use those methods when you have both the query and subject in memory.
IGD is preferred when you have a large static collection of BED files that you'll query many times against different user sets, and you want the index persisted on disk.

IGD in R (gtars)

Creating an IGD database

Example

Searching an IGD database

Example

Relationship to other gtars R functions

See also