AtomicList {IRanges} | R Documentation

## Lists of Atomic Vectors in Natural and Rle Form

### 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)

[Package IRanges version 2.14.12 Index]