Selection of ranges and columns
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.
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.
RangedSelection(ranges=IRangesList(),
colnames = character()): Constructors a RangedSelection
with the given ranges and colnames.
as(from, "RangedSelection"): Coerces from to a
RangedSelection object. Typically, from is a
IntegerRangesList, the ranges of which become the
ranges in the new RangedSelection.
In the code snippets below, x is always a RangedSelection.
ranges(x), ranges(x) <- value: Gets or sets the
ranges, a IntegerRangesList, that select rows with
overlapping intervals.
colnames(x), colnames(x) <- value: Gets the
names, a character vector, indicating the columns.
Michael Lawrence
rl <- IRangesList(chr1 = IRanges(c(1, 5), c(3, 6))) RangedSelection(rl) as(rl, "RangedSelection") # same as above RangedSelection(rl, "score")
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