GenomicTuples (version 1.6.2)

GTuples-class: GTuples objects

Description

The GTuples class is a container for the genomic tuples and their associated annotations.

Other methods

item{}{ show(x): By default the show method displays 5 head and 5 tail elements. This can be changed by setting the global options showHeadLines and showTailLines. If the object length is less than (or equal to) the sum of these 2 options plus 1, then the full object is displayed. Note that these options also affect the display of GRanges, GAlignments and GAlignmentPairs objects (defined in the GenomicAlignments package), as well as other objects defined in the IRanges and Biostrings packages (e.g. IRanges and DNAStringSet objects). }

Details

GTuples extends GRanges as a container for genomic tuples rather than genomic ranges. GTuples is a vector of genomic locations and associated annotations. Each element in the vector is comprised of a sequence name, a tuple, a strand, and optional metadata columns (e.g. score, GC content, etc.). This information is stored in four components: [object Object],[object Object],[object Object],[object Object],[object Object]

See Also

GTuplesList-class, seqinfo, Vector-class, Rle-class, Ranges-class, DataFrame, GRanges-class, intra-tuple-methods, findOverlaps-methods, nearest-methods,

Examples

## Create example 4-tuples
  seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
  gt4 <- GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
                                c(1, 3, 2, 4)),
                 tuples = matrix(c(1:10, 2:11, 3:12, 4:13), ncol = 4),
                 strand = Rle(strand(c("-", "+", "*", "+", "-")),
                              c(1, 2, 2, 3, 2)),
                 score = 1:10, GC = seq(1, 0, length = 10), seqinfo = seqinfo)
  gt4
  
  ## Summarizing elements
  table(seqnames(gt4))
  sum(width(gt4))
  summary(mcols(gt4)[,"score"])
  
  ## Renaming the underlying sequences
  seqlevels(gt4)
  seqlevels(gt4) <- sub("chr", "Chrom", seqlevels(gt4))
  gt4
  seqlevels(gt4) <- sub("Chrom", "chr", seqlevels(gt4)) # revert
  
  ## Combining objects
  gt4_a <- GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
                                c(1, 3, 2, 4)),
                 tuples = matrix(c(1:10, 21:30, 31:40, 41:50), ncol = 4),
                 strand = Rle(strand(c("-", "+", "*", "+", "-")),
                              c(1, 2, 2, 3, 2)),
                 score = 1:10, seqinfo = seqinfo)
                 
  gt4_b <- GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
                                c(1, 3, 2, 4)),
                 tuples = matrix(c(101:110, 121:130, 131:140, 141:150), 
                                 ncol = 4),
                 strand = Rle(strand(c("-", "+", "*", "+", "-")),
                              c(1, 2, 2, 3, 2)),
                 score = 1:10, seqinfo = seqinfo)
                 
  some_gt4 <- c(gt4_a, gt4_b)

  ## all_gt4 <- c(gt4, gt4_a, gt4_b) ## (This would fail)
  all_gt4 <- c(gt4, gt4_a, gt4_b, ignore.mcols=TRUE)
  
  ## The number of lines displayed in the 'show' method
  ## are controlled with two global options.
  options("showHeadLines" = 7)
  options("showTailLines" = 2)
  all_gt4
  
  ## Revert to default values
  options("showHeadLines"=NULL)
  options("showTailLines"=NULL)
  
  ## Get the size of the tuples stored in the GTuples object
  size(gt4)
  
  ## Get the tuples
  tuples(gt4)
  
  ## Get the matrix of intra-pair distances (IPD)
  IPD(all_gt4)  
  
  ## Can't combine genomic tuples of different sizes
  gt1 <- GTuples('chr1', matrix(30:40))
  gt1
  ## Returns error
  c(gt4, gt1)

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