GenomeIntervals-constructor: Constructor function for genomeIntervals objects
In genomeIntervals: Operations on genomic intervals

Description Usage Arguments Details Value Author(s) See Also Examples

A user-friendly constructor function for creating both Genome_intervals and Genome_intervals_stranded objects.

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GenomeIntervals(chromosome, start, end, strand = NULL,
                inter.base = NULL, leftOpen = NULL,
                rightOpen = NULL, ...)

`chromosome`	character vector of chromosome names of the intervals; will become the `seqnames` of the resulting object
`start`	numeric or integer; start (left-most) coordinate of the intervals
`end`	numeric or integer; end (right-most) coordinate of the intervals
`strand`	chacter; specifies which strand the intervals are located on; if specified an object of class `Genome_intervals_stranded` is created; if `NULL` an object of class `Genome_intervals` is created
`inter.base`	logical; if `TRUE` an interval is located between the specified coordinates, instead of spanning them; useful for restriction-enzym cutting sites, for example.
`leftOpen`	logical; if `TRUE` an interval is left-open; if `NULL` all intervals are assumed to be left-closed.
`rightOpen`	logical; if `TRUE` an interval is right-open; if `NULL` all intervals are assumed to be right-closed.
`...`	any additional annotation for supplied intervals

The arguments chromosome, start, and end need to be of the same length, with the first element of each vector corresponding to the first interval, the second element to the second interval, and so on.

The same applies to strand, inter.base, leftOpen, rightOpen and any additional vectors in '...', if they are specified.

An object of class Genome_intervals or Genome_intervals_stranded depending on whether strand has been specified.

J. Toedling

Genome_intervals-class, Genome_intervals_stranded-class

  ## constructing a Genome_intervals object
  G <- GenomeIntervals(start=c(1,3,4,5,8,10), end=c(5,5,6,8,9,11),
                       chromosome=rep(c("chr2","chrX","chr1"), each=2),
                       leftOpen=rep(c(FALSE, FALSE, TRUE), 2))
  show(G)

  ## constructing a Genome_intervals_stranded object with
  ##  additional interval annotation
  GS <- GenomeIntervals(start=c(1,3,4,5,8,10), end=c(5,5,6,8,9,11),
                        chromosome=rep(c("chr2","chrX","chr1"), each=2),
                        strand=c("-","-","+","+","+","+"),
                        GC.content=round(runif(6), digits=2))
  show(GS)