MutableRanges (version 0.6.2)

MutableGRanges-class: MutableGRanges objects

Description

MutableGRanges is a virtual GenomicRanges derivative that has mutable state, the implementation of which is left to subclasses, like SimpleMutableGRanges. There is no copying when replacing the ranges, element metadata, strand or seqnames. This is useful for graphical user interfaces and visualization. See the documentation of GenomicRanges for most of the behaviors of this class.

See Also

GenomicRanges-class

Examples

gr <-
    MutableGRanges(seqnames =
            Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
            ranges =
            IRanges(1:10, width = 10:1, names = head(letters,10)),
            strand =
            Rle(strand(c("-", "+", "*", "+", "-")),
                c(1, 2, 2, 3, 2)),
            score = 1:10,
            GC = seq(1, 0, length=10))
  gr

  # Changing 'gr2' also changes 'gr'
  gr2 <- gr
  s <- start(gr)
  start(gr2) <- 1
  gr
  start(gr) <- s

  # Summarizing elements
  table(seqnames(gr))
  sum(width(gr))
  summary(elementMetadata(gr)[,"score"]) # or values(gr)
  coverage(gr)

  # Changing sequence name
  unique(seqnames(gr))
  seqnames(gr) <- sub("chr", "Chrom", seqnames(gr))
  gr

  # Intra-interval operations
  flank(gr, 10)
  resize(gr, 10)
  shift(gr, 1)

  # Inter-interval operations
  disjoin(gr)
  gaps(gr, start = 1, end = 10)
  range(gr)
  reduce(gr)
  
  # Combining objects
  gr2 <- MutableGRanges(seqnames=Rle(c('Chrom1', 'Chrom2', 'Chrom3'),
                                     c(3, 3, 4)),
                        IRanges(1:10, width=5), strand='-',
                        score=101:110, GC = runif(10))
  gr3 <- MutableGRanges(seqnames=Rle(c('Chrom1', 'Chrom2', 'Chrom3'),
                                     c(3, 4, 3)),
                        IRanges(101:110, width=10), strand='-',
                        score=21:30)
  some.gr <- c(gr, gr2)
  
  ## all.gr <- c(gr, gr2, gr3) ## (This would fail)
  all.gr <- c(gr, gr2, gr3, .ignoreElementMetadata=TRUE)