IntegerRangesList-class: IntegerRangesList objects
In Bioconductor/IRanges: Foundation of integer range manipulation in Bioconductor

IntegerRangesList-class

R Documentation

IntegerRangesList objects

Description

The IntegerRangesList virtual class is a general container for storing a list of IntegerRanges objects.

Most users are probably more interested in the IRangesList container, an IntegerRangesList derivative for storing a list of IRanges objects.

Details

The place of IntegerRangesList in the Vector class hierarchy:

                               Vector
                                 ^
                                 |
                                List
                                 ^
                                 |
                             RangesList
                              ^     ^
                             /       \
                            /         \
                           /           \
                          /             \
                         /               \
                        /                 \
         IntegerRangesList               GenomicRangesList
                ^                                 ^
                |                                 |
           IRangesList                       GRangesList
             ^     ^                           ^     ^
            /       \                         /       \
           /         \                       /         \
          /           \                     /           \
   SimpleIRangesList   \             SimpleGRangesList   \
            CompressedIRangesList             CompressedGRangesList

Note that the Vector class hierarchy has many more classes. In particular Vector, List, RangesList, and IntegerRangesList have other subclasses not shown here.

Accessors

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

All of these accessors collapse over the spaces:

start(x), start(x) <- value:: Get or set the starts of the ranges. When setting the starts, value can be an integer vector of length sum(elementNROWS(x)) or an IntegerList object of length length(x) and names names(x).
end(x), end(x) <- value:: Get or set the ends of the ranges. When setting the ends, value can be an integer vector of length sum(elementNROWS(x)) or an IntegerList object of length length(x) and names names(x).
width(x), width(x) <- value:: Get or set the widths of the ranges. When setting the widths, value can be an integer vector of length sum(elementNROWS(x)) or an IntegerList object of length length(x) and names names(x).
space(x):: Gets the spaces of the ranges as a character vector. This is equivalent to names(x), except each name is repeated according to the length of its element.

Coercion

In the code snippet below, x is an IntegerRangesList object.

as.data.frame(x, row.names = NULL, optional = FALSE, ..., value.name = "value", use.outer.mcols = FALSE, group_name.as.factor = FALSE):: Coerces x to a data.frame. See as.data.frame on the List man page for details (?List).

In the following code snippet, from is something other than a IntegerRangesList:

as(from, "IntegerRangesList"):: When from is a IntegerRanges, analogous to as.list on a vector.

Arithmetic Operations

Any arithmetic operation, such as x + y, x * y, etc, where x is a IntegerRangesList, is performed identically on each element. Currently, IntegerRanges supports only the * operator, which zooms the ranges by a numeric factor.

Author(s)

M. Lawrence & H. Pagès

Examples

## ---------------------------------------------------------------------
## Basic manipulation
## ---------------------------------------------------------------------

range1 <- IRanges(start=c(1, 2, 3), end=c(5, 2, 8))
range2 <- IRanges(start=c(15, 45, 20, 1), end=c(15, 100, 80, 5))
named <- IRangesList(one = range1, two = range2)
length(named) # 2
start(named) # same as start(c(range1, range2))
names(named) # "one" and "two"
named[[1]] # range1
unnamed <- IRangesList(range1, range2)
names(unnamed) # NULL

# edit the width of the ranges in the list
edited <- named
width(edited) <- rep(c(3,2), elementNROWS(named))
edited

# same as list(range1, range2)
as.list(IRangesList(range1, range2))

# coerce to data.frame
as.data.frame(named)

IRangesList(range1, range2)

## zoom in 2X
collection <- IRangesList(one = range1, range2)
collection * 2

Bioconductor/IRanges documentation built on Feb. 11, 2024, 8:11 p.m.