GenomicData: Data on a Genome

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

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)

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.