GRangesList-class {GenomicRanges} | R Documentation

## GRangesList objects

### Description

The GRangesList class is a container for storing a collection of GRanges objects. It is a subclass of GenomicRangesList. It exists in 2 flavors: SimpleGRangesList and CompressedGRangesList. Each flavor uses a particular internal representation. The CompressedGRangesList flavor is the default. It is particularly efficient for storing a large number of list elements and operating on them.

### Constructors

`GRangesList(..., compress=TRUE)`:

  Creates a GRangesList object using the GRanges objects supplied in `...`, either consecutively or in a list. By default a CompressedGRangesList instance is returned, that is, a GRangesList object of the CompressedGRangesList flavor. Use `compress=FALSE` to get a SimpleGRangesList instance instead.

`makeGRangesListFromFeatureFragments(seqnames=Rle(factor()), fragmentStarts=list(), fragmentEnds=list(), fragmentWidths=list(), strand=character(0), sep=",")`:

  Constructs a GRangesList object from a list of fragmented features. See the Examples section below.

### Accessors

In the code snippets below, `x` is a GRangesList object.

`length(x)`:

  Get the number of list elements.

`names(x)`, `names(x) <- value`:

  Get or set the names on `x`.

`seqnames(x)`, `seqnames(x) <- value`:

  Get or set the sequence names in the form of an RleList. `value` can be an RleList or CharacterList object.

`ranges(x, use.mcols=FALSE)`, `ranges(x) <- value`:

  Get or set the ranges in the form of a CompressedIRangesList. `value` can be an IntegerRangesList object.

`start(x)`, `start(x) <- value`:

  Get or set `start(ranges(x))`.

`end(x)`, `end(x) <- value`:

  Get or set `end(ranges(x))`.

`width(x)`, `width(x) <- value`:

  Get or set `width(ranges(x))`.

`strand(x)`, `strand(x) <- value`:

  Get or set the strand in the form of an RleList object. `value` can be an RleList, CharacterList or single character. `value` as a single character converts all ranges in `x` to the same `value`; for selective strand conversion (i.e., mixed `+` and `-`) use RleList or CharacterList.

`mcols(x, use.names=FALSE)`, `mcols(x) <- value`:

  Get or set the metadata columns. `value` can be `NULL`, or a data.frame-like object (i.e. DataFrame or data.frame) holding element-wise metadata.

`elementNROWS(x)`:

  Get a vector of the `length` of each of the list element.

`isEmpty(x)`:

  Returns a logical indicating either if the GRangesList has no elements or if all its elements are empty.

`seqinfo(x)`, `seqinfo(x) <- value`:

  Get or set the information about the underlying sequences. `value` must be a Seqinfo object.

`seqlevels(x)`, `seqlevels(x, pruning.mode=c("error", "coarse", "fine", "tidy")) <- value`:

  Get or set the sequence levels. `seqlevels(x)` is equivalent to `seqlevels(seqinfo(x))` or to `levels(seqnames(x))`, those 2 expressions being guaranteed to return identical character vectors on a GRangesList object. `value` must be a character vector with no NAs. See `?seqlevels` for more information.

`seqlengths(x)`, `seqlengths(x) <- value`:

  Get or set the sequence lengths. `seqlengths(x)` is equivalent to `seqlengths(seqinfo(x))`. `value` can be a named non-negative integer or numeric vector eventually with NAs.

`isCircular(x)`, `isCircular(x) <- value`:

  Get or set the circularity flags. `isCircular(x)` is equivalent to `isCircular(seqinfo(x))`. `value` must be a named logical vector eventually with NAs.

`genome(x)`, `genome(x) <- value`:

  Get or set the genome identifier or assembly name for each sequence. `genome(x)` is equivalent to `genome(seqinfo(x))`. `value` must be a named character vector eventually with NAs.

`seqlevelsStyle(x)`, `seqlevelsStyle(x) <- value`:

  Get or set the seqname style for `x`. See the seqlevelsStyle generic getter and setter in the GenomeInfoDb package for more information.

`score(x), score(x) <- value`:

  Get or set the `score` metadata column.

### Coercion

In the code snippets below, `x` is a GRangesList 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`).

`as.list(x, use.names = TRUE)`:

  Creates a list containing the elements of `x`.

`as(x, "IRangesList")`:

  Turns `x` into an IRangesList object.

When `x` is a `list` of `GRanges`, it can be coerced to a `GRangesList`.

`as(x, "GRangesList")`:

  Turns `x` into a `GRangesList`.

### Subsetting

In the following code snippets, `x` is a GRangesList object.

`x[i, j]`, `x[i, j] <- value`:

  Get or set elements `i` with optional metadata columns `mcols(x)[,j]`, where `i` can be missing; an NA-free logical, numeric, or character vector; a logical-Rle object, or an AtomicList object.

`x[[i]]`, `x[[i]] <- value`:

  Get or set element `i`, where `i` is a numeric or character vector of length 1.

`x$name`, `x$name <- value`:

  Get or set element `name`, where `name` is a name or character vector of length 1.

`head(x, n = 6L)`:

  If `n` is non-negative, returns the first n elements of the GRangesList object. If `n` is negative, returns all but the last `abs(n)` elements of the GRangesList object.

`rep(x, times, length.out, each)`:

  Repeats the values in `x` through one of the following conventions:

  `times`

    Vector giving the number of times to repeat each element if of length `length(x)`, or to repeat the whole vector if of length 1.

  `length.out`

    Non-negative integer. The desired length of the output vector.

  `each`

    Non-negative integer. Each element of `x` is repeated `each` times.

`subset(x, subset)`:

  Returns a new object of the same class as `x` made of the subset using logical vector `subset`, where missing values are taken as `FALSE`.

`tail(x, n = 6L)`:

  If `n` is non-negative, returns the last n list elements of the GRangesList object. If `n` is negative, returns all but the first `abs(n)` list elements of the GRangesList object.

### Combining

In the code snippets below, `x` is a GRangesList object.

`c(x, ...)`:

  Combines `x` and the GRangesList objects in `...` together. Any object in `...` must belong to the same class as `x`, or to one of its subclasses, or must be `NULL`. The result is an object of the same class as `x`.

`append(x, values, after = length(x))`:

  Inserts the `values` into `x` at the position given by `after`, where `x` and `values` are of the same class.

`unlist(x, recursive = TRUE, use.names = TRUE)`:

  Concatenates the elements of `x` into a single GRanges object.

### Looping

In the code snippets below, `x` is a GRangesList object.

`endoapply(X, FUN, ...)`:

  Similar to `lapply`, but performs an endomorphism, i.e. returns an object of `class(X)`.

`lapply(X, FUN, ...)`:

  Like the standard `lapply` function defined in the base package, the `lapply` method for GRangesList objects returns a list of the same length as `X`, with each element being the result of applying `FUN` to the corresponding element of `X`.

`Map(f, ...)`:

  Applies a function to the corresponding elements of given GRangesList objects.

`mapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE)`:

  Like the standard `mapply` function defined in the base package, the `mapply` method for GRangesList objects is a multivariate version of `sapply`.

`mendoapply(FUN, ..., MoreArgs = NULL)`:

  Similar to `mapply`, but performs an endomorphism across multiple objects, i.e. returns an object of `class(list(...)[[1]])`.

`Reduce(f, x, init, right = FALSE, accumulate = FALSE)`:

  Uses a binary function to successively combine the elements of `x` and a possibly given initial value.

  `f`

    A binary argument function.

  `init`

    An R object of the same kind as the elements of `x`.

  `right`

    A logical indicating whether to proceed from left to right (default) or from right to left.

  `nomatch`

    The value to be returned in the case when "no match" (no element satisfying the predicate) is found.

`sapply(X, FUN, ..., simplify=TRUE, USE.NAMES=TRUE)`:

  Like the standard `sapply` function defined in the base package, the `sapply` method for GRangesList objects is a user-friendly version of `lapply` by default returning a vector or matrix if appropriate.

### Author(s)

P. Aboyoun & H. Pagès

### See Also

- GRanges objects.

- `seqinfo` in the GenomeInfoDb package.

- IntegerRangesList objects in the IRanges package.

- RleList objects in the IRanges package.

- DataFrameList objects in the IRanges package.

- intra-range-methods, inter-range-methods, coverage-methods, setops-methods, and findOverlaps-methods.

- GenomicRangesList objects.

### Examples

    ## Construction with GRangesList():
    gr1 <- GRanges("chr2", IRanges(3, 6),
                   strand="+", score=5L, GC=0.45)
    gr2 <- GRanges(c("chr1", "chr1"), IRanges(c(7,13), width=3),
                   strand=c("+", "-"), score=3:4, GC=c(0.3, 0.5))
    gr3 <- GRanges(c("chr1", "chr2"), IRanges(c(1, 4), c(3, 9)),
                   strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
    grl <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
    grl

    ## Summarizing elements:
    elementNROWS(grl)
    table(seqnames(grl))

    ## Extracting subsets:
    grl[seqnames(grl) == "chr1", ]
    grl[seqnames(grl) == "chr1" & strand(grl) == "+", ]

    ## Renaming the underlying sequences:
    seqlevels(grl)
    seqlevels(grl) <- sub("chr", "Chrom", seqlevels(grl))
    grl

    ## Coerce to IRangesList (seqnames and strand information is lost):
    as(grl, "IRangesList")

    ## isDisjoint():
    isDisjoint(grl)

    ## disjoin():
    disjoin(grl)  # metadata columns and order NOT preserved

    ## Construction with makeGRangesListFromFeatureFragments():
    filepath <- system.file("extdata", "feature_frags.txt",
                            package="GenomicRanges")
    featfrags <- read.table(filepath, header=TRUE, stringsAsFactors=FALSE)
    grl2 <- with(featfrags,
                 makeGRangesListFromFeatureFragments(seqnames=targetName,
                                                     fragmentStarts=targetStart,
                                                     fragmentWidths=blockSizes,
                                                     strand=strand))
    names(grl2) <- featfrags$RefSeqID
    grl2

[Package GenomicRanges version 1.46.1 Index]