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GenomicCoordinates

Enhanced string parsing for genomic coordinates in Bioconductor.

Overview

GenomicCoordinates extends the string parsing capabilities of GenomicRanges, IRanges, and InteractionSet packages to support various genomic coordinate string formats including comma-separated numbers, space-delimited coordinates, and automatic detection of appropriate object types.

Installation 

# Install from Bioconductor (when available)
BiocManager::install("GenomicCoordinates")

# Or install version from github
BiocManager::install("js2264/GenomicCoordinates")

Supported Formats

  • Standard: chr1:1000-2000, chr1:1000-2000:+ (auto-detects as GPos)
  • Single positions: chr1:1000 (auto-detects as GPos)
  • Interactions: chr1:1-10|chr2:4-40 (auto-detects as GInteractions)
  • Comma-separated: chr1:1,000-2,000, chr1:100,000-200,000
  • Space-delimited: chr1 1000 2000
  • Irregular spacing: chr1 1000 2000, chr1: 1-10 | chr2: 20-30

Quick Start

Loading the GenomicCoordinates package allows you to use enhanced parsing methods directly:

library(GenomicRanges)
GRanges("chr1:100,000-200,000")
## Error in asMethod(object) : 
##   The character vector to convert to a GRanges object must contain strings of the form "chr:start-end" or "chr:start-end:strand", with end >= start - 1, or "chr:pos" or "chr:pos:strand". For example: "chr1:2501-2900", "chr1:2501-2900:+",
##   or "chr1:740". Note that ".." is a valid alternate start/end separator. Strand can be "+", "-", "*", or missing.
  
library(GenomicCoordinates)
GRanges("chr1:100,000-200,000")
## Ranges object with 1 range and 0 metadata columns:
##      seqnames        ranges strand
##         <Rle>     <IRanges>  <Rle>
##  [1]     chr1 100000-200000      *
##  -------
##  seqinfo: 1 sequence from an unspecified genome; no seqlengths
# Enhanced GRanges parsing
GRanges("chr1 1000 2000")

# Auto-detection
GenomicCoordinates("chr1:1000")  # Returns GPos

# GInteractions
as("chr1:1-10|chr2:4-40", "GInteractions")

# Enhanced IRanges
IRanges("1,234..56,345")