Data on a Genome
The rtracklayer package adds
convenience methods on top of GenomicRanges and IntegerRangesList
to manipulate data on genomic ranges.
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.
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.
Michael Lawrence and Patrick Aboyoun
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.