Constructor function for genomeIntervals objects

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Description

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

Usage

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

Arguments

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

Details

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.

Value

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

Author(s)

J. Toedling

See Also

Genome_intervals-class, Genome_intervals_stranded-class

Examples

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  ## 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)