RangedSelection-class {IRanges} | R Documentation |
Selection of ranges and columns
Description
A RangedSelection
represents a query against a table
of interval data in terms of ranges and column names. The ranges
select any table row with an overlapping interval. Note that the
intervals are always returned, even if no columns are selected.
Details
Traditionally, tabular data structures have supported the
subset
function, which allows one to select a subset of
the rows and columns from the table. In that case, the rows and
columns are specified by two separate arguments. As querying interval
data sources, especially those external to R, such as binary indexed
files and databases, is increasingly common, there is a need to
encapsulate the row and column specifications into a single data
structure, mostly for the sake of interface
cleanliness. The RangedSelection
class fills that role.
Constructor
RangedSelection(ranges=IRangesList(), colnames = character())
: Constructors aRangedSelection
with the givenranges
andcolnames
.
Coercion
as(from, "RangedSelection")
: Coercesfrom
to aRangedSelection
object. Typically,from
is aIntegerRangesList
, the ranges of which become the ranges in the newRangedSelection
.
Accessors
In the code snippets below, x
is always a RangedSelection
.
ranges(x), ranges(x) <- value
: Gets or sets the ranges, aIntegerRangesList
, that select rows with overlapping intervals.colnames(x), colnames(x) <- value
: Gets the names, acharacter
vector, indicating the columns.
Author(s)
Michael Lawrence
Examples
rl <- IRangesList(chr1 = IRanges(c(1, 5), c(3, 6)))
RangedSelection(rl)
as(rl, "RangedSelection") # same as above
RangedSelection(rl, "score")