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Normalize an object representing genomic ranges

Source: R/errorChecking.R
normalize_ranges.Rd

Normalize an object representing genomic ranges

Usage

normalize_ranges(
  ranges,
  metadata_cols = character(0),
  zero_based_coords = !is(ranges, "GRanges"),
  n = 1
)

Arguments

ranges

Genomic regions given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

  • chr, start, end: genomic position

metadata_cols

Optional list of metadata columns to require & extract

zero_based_coords

If true, coordinates start and 0 and the end coordinate is not included in the range. If false, coordinates start at 1 and the end coordinate is included in the range

Value

data frame with zero-based coordinates, and elements chr (factor), start (int), and end (int). If ranges does not have chr level information, chr levels are the sorted unique values of chr.

If strand is in metadata_cols, then the output strand element will be TRUE for positive strand, and FALSE for negative strand. (Converted from a character vector of "+"/"-" if necessary)