Package 'GenomicCoordinates'

Handle special genomic string formats

Description

Handle special genomic string formats

Usage

.handle_special_formats(x)

Arguments

x	Character string

Value

Parsed genomic information

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Additional helper functions for corner cases

Description

Handle various edge cases and special formats in genomic coordinate parsing Detect if a string represents a single genomic position

Usage

.is_single_position(x)

Arguments

x	Character string

Value

Logical indicating if it's a single position

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Convert to GPos object

Description

Converts character strings representing single genomic positions to GPos objects.

Usage

as_gpos(.data, ...)

Arguments

.data	A character vector of genomic position strings
...	Additional arguments (unused)

Value

A GPos object

Examples

as_gpos("chr1:1000")
as_gpos("chr1:1,000:+")
as_gpos(c("chr1:1000", "chr2:2000", "chr3:3000"))

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Conversion methods for genomic coordinates

Description

Methods to convert character strings to GRanges, GPos, and GInteractions objects with support for various string formats including comma-separated numbers and space-delimited coordinates.

Extensions to IRanges parsing to handle comma-separated numbers and space-delimited coordinates.

Usage

## S4 method for signature 'character'
as_granges(.data, ..., keep_mcols = TRUE)

## S4 method for signature 'character'
as_gpos(.data, ...)

## S4 method for signature 'character'
as_ginteractions(
  .data,
  ...,
  keep.extra.columns = TRUE,
  starts.in.df.are.0based = FALSE
)

## S4 method for signature 'character'
as_iranges(.data, ..., keep_mcols = TRUE)

Arguments

.data	A character vector of coordinate strings
...	Additional arguments (unused)
keep_mcols	Ignored for character input (included for generic compatibility with plyranges)
keep.extra.columns	Ignored for character input (included for generic compatibility with plyinteractions)
starts.in.df.are.0based	Ignored for character input (included for generic compatibility with plyinteractions)

Value

The appropriate Bioconductor object type

An IRanges object

Examples

# GRanges conversion
as_granges("chr1:1000-2000")
as_granges("chr1:1,000-2,000:+")
as_granges(c("chr1:1000-2000", "chr2:3000-4000"))

# GPos conversion
as_gpos("chr1:1000")
as_gpos(c("chr1:1000", "chr2:2000"))

# GInteractions conversion
as_ginteractions("chr1:1-10|chr2:20-30")

as_iranges("1000-2000")
as_iranges("1,000-2,000")
as_iranges(c("100-200", "300-400"))

---

Detect the appropriate class for genomic strings

Description

Utility function to determine what class a genomic string should be parsed as, without actually performing the parsing.

Usage

detect_genomic_class(x)

Arguments

x	Character string or vector

Value

Character vector of predicted classes

Examples

detect_genomic_class("chr1:1000-2000")
detect_genomic_class("chr1:1000")
detect_genomic_class(c("chr1:1-10|chr2:20-30", "1000-2000"))

---

GenomicCoordinates: Main parsing function

Description

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")

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.

Value

GRanges, GPos, GInteractions, or IRanges object

Examples

# Auto-detection examples
GenomicCoordinates("chr1:1000-2000")           # Returns GRanges
GenomicCoordinates("chr1:1000")                # Returns GPos  
GenomicCoordinates("chr1:1-10|chr2:4-40")      # Returns GInteractions
GenomicCoordinates("1000-2000")               # Returns IRanges

# Force specific class
GenomicCoordinates("chr1:1000", force_class = "GRanges")

# Enhanced format support
GenomicCoordinates("chr1:100,000-200,000")     # Comma-separated
GenomicCoordinates("chr1 1000 2000")           # Space-delimited

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Re-exported functions from plyranges and plyinteractions

Description

These generics are re-exported from plyranges and plyinteractions to provide conversion functions for character strings.

Usage

as_granges(.data, ..., keep_mcols = TRUE)

as_iranges(.data, ..., keep_mcols = TRUE)

as_ginteractions(
  .data,
  ...,
  keep.extra.columns = TRUE,
  starts.in.df.are.0based = FALSE
)

Arguments

.data	Object to convert
...	Additional arguments passed to methods
keep_mcols	Logical; whether to keep metadata columns (plyranges)
keep.extra.columns	Logical; whether to keep extra columns (plyinteractions)
starts.in.df.are.0based	Logical; whether starts are 0-based (plyinteractions)

Value

A Bioconductor object

Examples

as_granges("chr1:1000-2000")
as_iranges("1000-2000")
as_ginteractions("chr1:1-10|chr2:20-30")

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