GenomicData {rtracklayer} | R Documentation

## Data on a Genome

### Description

The `rtracklayer` package adds convenience methods on top of `GenomicRanges` and `IntegerRangesList` to manipulate data on genomic ranges.

### Accessors

In the code snippets below, `x` is a `GenomicRanges` or `IntegerRangesList` object.

  `chrom(x), chrom(x) <- value`: Gets or sets the chromosome names for `x`. The length of `value` should equal the length of `x`.

  `score(x)`: Gets the “score” column from the element metadata of a `GenomicRanges` or `GRangesList`. Many track formats have a score column, so this is often used during export. The `ANY` fallback for this method simply returns `NULL`.

### Constructor

  `GenomicData(ranges, ..., strand = NULL, chrom = NULL, genome = NULL)`: Constructs a `GRanges` instance with the given `ranges` and variables in `...` (see the `GRanges` constructor).

  If non-`NULL`, the `strand` argument specifies the strand of each range. It should be a character vector or factor of length equal to that of `ranges`. All values should be either `-`, `+`, or `*`. To get the levels for `strand`, call `levels(strand())`.

  `chrom` argument is analogous to `seqnames` in the `GRanges` constructor.

  The `genome` argument should be a scalar string. See the examples.

### Author(s)

Michael Lawrence and Patrick Aboyoun

### Examples

      range1 <- IRanges(c(1,2,3), c(5,2,8))

      ## with some data ##
      filter <- c(1L, 0L, 1L)
      score <- c(10L, 2L, NA)
      strand <- factor(c("+", NA, "-"), levels = levels(strand()))
      ## GRanges instance
      gr <- GenomicData(range1, score, chrom = "chr1", genome = "hg18")
      mcols(gr)[["score"]]
      strand(gr) ## all '*'
      gr <- GenomicData(range1, score, filt = filter, strand = strand,
                        chrom = "chr1")
      mcols(gr)[["filt"]]
      strand(gr) ## equal to 'strand'
      ## coercion from data.frame ##
      df <- as.data.frame(gr)

[Package rtracklayer version 1.52.1 Index]