GenomicCoordinates: Main parsing function

Automatically parse genomic coordinate strings into the most appropriate Bioconductor object type (GRanges, GPos, GInteractions, or IRanges). Parse strings into appropriate genomic objects

Usage

GenomicCoordinates(x, force_class = NULL)

Arguments

x

Character string or vector of genomic coordinates

force_class

Optional class to force ("GRanges", "GPos", "GInteractions", "IRanges")

Value

GRanges, GPos, GInteractions, or IRanges object

Details

This is the main function of the GenomicCoordinates package. It automatically detects the most appropriate object type based on the input string format and returns the corresponding Bioconductor object.

Examples

# Auto-detection examples
GenomicCoordinates("chr1:1000-2000")           # Returns GRanges
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1 1000-2000      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
GenomicCoordinates("chr1:1000")                # Returns GPos  
#> UnstitchedGPos object with 1 position and 0 metadata columns:
#>       seqnames       pos strand
#>          <Rle> <integer>  <Rle>
#>   [1]     chr1      1000      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
GenomicCoordinates("chr1:1-10|chr2:4-40")      # Returns GInteractions
#> GInteractions object with 1 interaction and 0 metadata columns:
#>       seqnames1   ranges1 strand1     seqnames2   ranges2 strand2
#>           <Rle> <IRanges>   <Rle>         <Rle> <IRanges>   <Rle>
#>   [1]      chr1      1-10       * ---      chr2      4-40       *
#>   -------
#>   regions: 2 ranges and 0 metadata columns
#>   seqinfo: 2 sequences from an unspecified genome; no seqlengths
GenomicCoordinates("1000-2000")               # Returns IRanges
#> IRanges object with 1 range and 0 metadata columns:
#>           start       end     width
#>       <integer> <integer> <integer>
#>   [1]      1000      2000      1001

# Force specific class
GenomicCoordinates("chr1:1000", force_class = "GRanges")
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1      1000      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# Enhanced format support
GenomicCoordinates("chr1:100,000-200,000")     # Comma-separated
#> GRanges 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
GenomicCoordinates("chr1 1000 2000")           # Space-delimited
#> GRanges object with 1 range and 0 metadata columns:
#>       seqnames    ranges strand
#>          <Rle> <IRanges>  <Rle>
#>   [1]     chr1 1000-2000      *
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths