AtomicList-class: Lists of Atomic Vectors in Natural and Rle Form

In IRanges: Foundation of integer range manipulation in Bioconductor

Description

An extension of List that holds only atomic vectors in either a natural or run-length encoded form.

Details

The lists of atomic vectors are LogicalList, IntegerList, NumericList, ComplexList, CharacterList, and RawList. There is also an RleList class for run-length encoded versions of these atomic vector types.

Each of the above mentioned classes is virtual with Compressed* and Simple* non-virtual representations.

Constructors

LogicalList(..., compress = TRUE): Concatenates the logical vectors in ... into a new LogicalList. If compress, the internal storage of the data is compressed.

IntegerList(..., compress = TRUE): Concatenates the integer vectors in ... into a new IntegerList. If compress, the internal storage of the data is compressed.

NumericList(..., compress = TRUE): Concatenates the numeric vectors in ... into a new NumericList. If compress, the internal storage of the data is compressed.

ComplexList(..., compress = TRUE): Concatenates the complex vectors in ... into a new ComplexList. If compress, the internal storage of the data is compressed.

CharacterList(..., compress = TRUE): Concatenates the character vectors in ... into a new CharacterList. If compress, the internal storage of the data is compressed.

RawList(..., compress = TRUE): Concatenates the raw vectors in ... into a new RawList. If compress, the internal storage of the data is compressed.

RleList(..., compress = TRUE): Concatenates the run-length encoded atomic vectors in ... into a new RleList. If compress, the internal storage of the data is compressed.

FactorList(..., compress = TRUE): Concatenates the factor objects in ... into a new FactorList. If compress, the internal storage of the data is compressed.

Coercion

as(from, "CompressedSplitDataFrameList"), as(from, "SimpleSplitDataFrameList"): Creates a CompressedSplitDataFrameList/SimpleSplitDataFrameList instance from an AtomicList instance.

as(from, "IRangesList"), as(from, "CompressedIRangesList"), as(from, "SimpleIRangesList"): Creates a CompressedIRangesList/SimpleIRangesList instance from a LogicalList or logical RleList instance. Note that the elements of this instance are guaranteed to be normal.

as(from, "NormalIRangesList"), as(from, "CompressedNormalIRangesList"), as(from, "SimpleNormalIRangesList"): Creates a CompressedNormalIRangesList/SimpleNormalIRangesList instance from a LogicalList or logical RleList instance.

as(from, "CharacterList"), as(from, "ComplexList"), as(from, "IntegerList"), as(from, "LogicalList"), as(from, "NumericList"), as(from, "RawList"), as(from, "RleList"): Coerces an AtomicList from to another derivative of AtomicList.

as(from, "AtomicList"): If from is a vector, converts it to an AtomicList of the appropriate type.

drop(x): Checks if every element of x is of length one, and, if so, unlists x. Otherwise, an error is thrown.

as(from, "RleViews"): Creates an RleViews where each view corresponds to an element of from. The subject is unlist(from).

as.matrix(x, col.names=NULL): Maps the elements of the list to rows of a matrix. The column mapping depends on whether there are inner names (either on the object or provided via col.names as a List object). If there are no inner names, each row is padded with NAs to reach the length of the longest element. If there are inner names, there is a column for each unique name and the mapping is by name. To provide inner names, the col.names argument should be a List, usually a CharacterList or FactorList (which is particularly efficient). If col.names is a character vector, it names the columns of the result, but does not imply inner names.

Compare, Order, Tabulate

The following methods are provided for element-wise comparison of 2 AtomicList objects, and ordering or tabulating of each list element of an AtomicList object: is.na, duplicated, unique, match, %in%, table, order, sort.

RleList Methods

RleList has a number of methods that are not shared by other AtomicList derivatives.

runLength(x): Gets the run lengths of each element of the list, as an IntegerList.

runValue(x), runValue(x) <- value: Gets or sets the run values of each element of the list, as an AtomicList.

ranges(x): Gets the run ranges as a IntegerRangesList.

Author(s)

P. Aboyoun

See Also

• AtomicList-utils for common operations on AtomicList objects.

• List objects in the S4Vectors package for the parent class.

Examples

int1 <- c(1L,2L,3L,5L,2L,8L)
int2 <- c(15L,45L,20L,1L,15L,100L,80L,5L)
collection <- IntegerList(int1, int2)

## names
names(collection) <- c("one", "two")
names(collection)
names(collection) <- NULL # clear names
names(collection)
names(collection) <- "one"
names(collection) # c("one", NA)

## extraction
collection[[1]] # range1
collection[["1"]] # NULL, does not exist
collection[["one"]] # range1
collection[[NA_integer_]] # NULL

## subsetting
collection[numeric()] # empty
collection[NULL] # empty
collection[] # identity
collection[c(TRUE, FALSE)] # first element
collection[2] # second element
collection[c(2,1)] # reversed
collection[-1] # drop first
collection$one

## replacement
collection$one <- int2
collection[[2]] <- int1

## concatenating
col1 <- IntegerList(one = int1, int2)
col2 <- IntegerList(two = int2, one = int1)
col3 <- IntegerList(int2)
append(col1, col2)
append(col1, col2, 0)
col123 <- c(col1, col2, col3)
col123

## revElements
revElements(col123)
revElements(col123, 4:5)

IRanges documentation built on Dec. 14, 2020, 2 a.m.