GRanges-class {GenomicRanges} | R Documentation

## GRanges objects

### Description

The GRanges class is a container for the genomic locations and their associated annotations.

### Details

GRanges is a vector of genomic locations and associated annotations. Each element in the vector is comprised of a sequence name, an interval, a strand, and optional metadata columns (e.g. score, GC content, etc.). This information is stored in four components:

`seqnames`

  a 'factor' Rle object containing the sequence names.

`ranges`

  an IRanges object containing the ranges.

`strand`

  a 'factor' Rle object containing the strand information.

`mcols`

  a DataFrame object containing the metadata columns. Columns cannot be named `"seqnames"`, `"ranges"`, `"strand"`, `"seqlevels"`, `"seqlengths"`, `"isCircular"`, `"start"`, `"end"`, `"width"`, or `"element"`.

`seqinfo`

  a Seqinfo object containing information about the set of genomic sequences present in the GRanges object.

### Constructor

  `GRanges(seqnames=NULL, ranges=NULL, strand=NULL, ..., seqinfo=NULL, seqlengths=NULL)`: Creates a GRanges object.

  `seqnames`

    `NULL`, or an Rle object, character vector, or factor containing the sequence names.

  `ranges`

    `NULL`, or an IRanges object containing the ranges.

  `strand`

    `NULL`, or an Rle object, character vector, or factor containing the strand information.

  `...`

    Metadata columns to set on the GRanges object. All the metadata columns must be vector-like objects of the same length as the object to construct. They cannot be named `"start"`, `"end"`, `"width"`, or `"element"`.

  `seqinfo`

    Either `NULL`, or a Seqinfo object, or a character vector of unique sequence names (a.k.a. seqlevels), or a named numeric vector of sequence lengths. When not `NULL`, `seqinfo` must be compatible with the sequence names in `seqnames`, that is, it must have one entry for each unique sequence name in `seqnames`. Note that it can have additional entries i.e. entries for seqlevels not present in `seqnames`.

  `seqlengths`

    `NULL`, or an integer vector named with `levels(seqnames)` and containing the lengths (or NA) for each level in `levels(seqnames)`.

  If `ranges` is not supplied and/or NULL then the constructor proceeds in 2 steps:

  1. An initial GRanges object is created with `as(seqnames, "GRanges")`.

  2. Then this GRanges object is updated according to whatever non-NULL remaining arguments were passed to the call to `GRanges()`.

  As a consequence of this behavior, `GRanges(x)` is equivalent to `as(x, "GRanges")`.

### Accessors

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

  `length(x)`: Get the number of elements.

  `seqnames(x)`, `seqnames(x) <- value`: Get or set the sequence names. `value` can be an Rle object, a character vector, or a factor.

  `ranges(x)`, `ranges(x) <- value`: Get or set the ranges. `value` can be an IntegerRanges 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. `value` can be an Rle object, character vector, or factor.

  `names(x)`, `names(x) <- value`: Get or set the names of the elements.

  `mcols(x, use.names=FALSE)`, `mcols(x) <- value`: Get or set the metadata columns. If `use.names=TRUE` and the metadata columns are not `NULL`, then the names of `x` are propagated as the row names of the returned DataFrame object. When setting the metadata columns, the supplied value must be `NULL` or a data.frame-like object (i.e. DataTable or data.frame) object holding element-wise metadata.

  `elementMetadata(x)`, `elementMetadata(x) <- value`, `values(x)`, `values(x) <- value`: Alternatives to `mcols` functions. Their use is discouraged.

  `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 GRanges 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” column from the element metadata.

  `granges(x, use.names=FALSE, use.mcols=FALSE)`: Squeeze the genomic ranges out of GenomicRanges object `x` and return them in a GRanges object parallel to `x` (i.e. same length as `x`). If `use.mcols` is `TRUE`, the metadata columns are propagated. If `x` is a GenomicRanges derivative with extra column slots, these will be propagated as metadata columns on the returned GRanges object.

### Coercion

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

  `as(from, "GRanges")`: Creates a GRanges object from a character vector, a factor, or IntegerRangesList object.

  When `from` is a character vector (or a factor), each element in it must represent a genomic range in format `chr1:2501-2800` (unstranded range) or `chr1:2501-2800:+` (stranded range). `..` is also supported as a separator between the start and end positions. Strand can be `+`, `-`, `*`, or missing. The names on `from` are propagated to the returned GRanges object. See `as.character()` and `as.factor()` below for the reverse transformations.

  Coercing a data.frame or DataFrame into a GRanges object is also supported. See `makeGRangesFromDataFrame` for the details.

  `as(from, "RangedData")`: Creates a RangedData object from a GRanges object. The `strand` and metadata columns become columns in the result. The `seqlengths(from)`, `isCircular(from)`, and `genome(from)` vectors are stored in the metadata columns of `ranges(rd)`.

  `as(from, "IntegerRangesList")`: Creates a IntegerRangesList object from a GRanges object. The `strand` and metadata columns become inner metadata columns (i.e. metadata columns on the ranges). The `seqlengths(from)`, `isCircular(from)`, and `genome(from)` vectors become the metadata columns.

  `as.character(x, ignore.strand=FALSE)`: Turn GRanges object `x` into a character vector where each range in `x` is represented by a string in format `chr1:2501-2800:+`. If `ignore.strand` is TRUE or if all the ranges in `x` are unstranded (i.e. their strand is set to `*`), then all the strings in the output are in format `chr1:2501-2800`.

  The names on `x` are propagated to the returned character vector. Its metadata (`metadata(x)`) and metadata columns (`mcols(x)`) are ignored.

  See `as(from, "GRanges")` above for the reverse transformation.

  `as.factor(x)`: Equivalent to

        factor(as.character(x), levels=as.character(sort(unique(x))))

  See `as(from, "GRanges")` above for the reverse transformation.

  Note that `table(x)` is supported on a GRanges object. It is equivalent to, but much faster than, `table(as.factor(x))`.

  `as.data.frame(x, row.names = NULL, optional = FALSE, ...)`: Creates a data.frame with columns `seqnames` (factor), `start` (integer), `end` (integer), `width` (integer), `strand` (factor), as well as the additional metadata columns stored in `mcols(x)`. Pass an explicit `stringsAsFactors=TRUE/FALSE` argument via `...` to override the default conversions for the metadata columns in `mcols(x)`.

  `as(from, "Grouping")`: Creates a `ManyToOneGrouping` object that groups `from` by seqname, strand, start and end (same as the default sort order). This makes it convenient, for example, to aggregate a GenomicRanges object by range.

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

  `as(x, "GRanges")`, `as(x, "GenomicRanges")`, `as(x, "IntegerRangesList")`: Turns Seqinfo object `x` (with no `NA` lengths) into a GRanges or IntegerRangesList.

### Subsetting

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

  `x[i]`: Return a new GRanges object made of the elements selected by `i`.

  `x[i, j]`: Like the above, but allow the user to conveniently subset the metadata columns thru `j`.

  `x[i] <- value`: Replacement version of `x[i]`.

  `x$name`, `x$name <- value`: Shortcuts for `mcols(x)$name` and `mcols(x)$name <- value`, respectively. Provided as a convenience, for GRanges objects *only*, and as the result of strong popular demand. Note that those methods are not consistent with the other `$` and `$<-` methods in the IRanges/GenomicRanges infrastructure, and might confuse some users by making them believe that a GRanges object can be manipulated as a data.frame-like object. Therefore we recommend using them only interactively, and we discourage their use in scripts or packages. For the latter, use `mcols(x)$name` and `mcols(x)$name <- value`, instead of `x$name` and `x$name <- value`, respectively.

See `?`[`` in the S4Vectors package for more information about subsetting Vector derivatives and for an important note about the `x[i, j]` form.

Note that a GRanges object can be used as a subscript to subset a list-like object that has names on it. In that case, the names on the list-like object are interpreted as sequence names. In the code snippets below, `x` is a list or List object with names on it, and the subscript `gr` is a GRanges object with all its seqnames being valid `x` names.

  `x[gr]`: Return an object of the same class as `x` and parallel to `gr`. More precisely, it's conceptually doing:

        lapply(gr, function(gr1) x[[seqnames(gr1)]][ranges(gr1)])

### Concatenation

  `c(x, ..., ignore.mcols=FALSE)`: Concatenate GRanges object `x` and the GRanges objects in `...` together. See `?c` in the S4Vectors package for more information about concatenating Vector derivatives.

### Splitting

  `split(x, f, drop=FALSE)`: Splits GRanges object `x` according to `f` to create a GRangesList object. If `f` is a list-like object then `drop` is ignored and `f` is treated as if it was `rep(seq_len(length(f)), sapply(f, length))`, so the returned object has the same shape as `f` (it also receives the names of `f`). Otherwise, if `f` is not a list-like object, empty list elements are removed from the returned object if `drop` is `TRUE`.

### Displaying

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

  `show(x)`: By default the `show` method displays 5 head and 5 tail elements. This can be changed by setting the global options `showHeadLines` and `showTailLines`. If the object length is less than (or equal to) the sum of these 2 options plus 1, then the full object is displayed. Note that these options also affect the display of GAlignments and GAlignmentPairs objects (defined in the GenomicAlignments package), as well as other objects defined in the IRanges and Biostrings packages (e.g. IRanges and DNAStringSet objects).

### Author(s)

P. Aboyoun and H. Pagès

### See Also

- The IRanges class in the IRanges package for storing a set of integer ranges.

- The GPos class for representing a set of genomic positions (i.e. genomic ranges of width 1, a.k.a. genomic loci).

- `makeGRangesFromDataFrame` for making a GRanges object from a data.frame or DataFrame object.

- Seqinfo objects and the `seqinfo` accessor and family in the GenomeInfoDb package for accessing/modifying information about the underlying sequences of a GenomicRanges derivative.

- GenomicRanges-comparison for comparing and ordering genomic ranges and/or positions.

- findOverlaps-methods for finding overlapping genomic ranges and/or positions.

- intra-range-methods and inter-range-methods for intra range and inter range transformations of GenomicRanges derivatives.

- coverage-methods for computing the coverage of a set of genomic ranges and/or positions.

- setops-methods for set operations on GRanges objects.

- nearest-methods for finding the nearest genomic range/position neighbor.

- `absoluteRanges` for transforming genomic ranges into absolute ranges (i.e. into ranges on the sequence obtained by virtually concatenating all the sequences in a genome).

- `tileGenome` for putting tiles on a genome.

- genomicvars for manipulating genomic variables.

- GRangesList objects.

- Vector, Rle, and DataFrame objects in the S4Vectors package.

### Examples

    showClass("GRanges")  # shows the known subclasses

    ## ---------------------------------------------------------------------
    ## CONSTRUCTION
    ## ---------------------------------------------------------------------
    ## Specifying the bare minimum i.e. seqnames and ranges only. The
    ## GRanges object will have no names, no strand information, and no
    ## metadata columns:
    gr0 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
                   IRanges(1:10, width=10:1))
    gr0

    ## Specifying names, strand, metadata columns. They can be set on an
    ## existing object:
    names(gr0) <- head(letters, 10)
    strand(gr0) <- Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2))
    mcols(gr0)$score <- 1:10
    mcols(gr0)$GC <- seq(1, 0, length=10)
    gr0

    ## ... or specified at construction time:
    gr <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
                  IRanges(1:10, width=10:1, names=head(letters, 10)),
                  Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
                  score=1:10, GC=seq(1, 0, length=10))
    stopifnot(identical(gr0, gr))

    ## Specifying the seqinfo. It can be set on an existing object:
    seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
    seqinfo(gr0) <- merge(seqinfo(gr0), seqinfo)
    seqlevels(gr0) <- seqlevels(seqinfo)

    ## ... or specified at construction time:
    gr <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
                  IRanges(1:10, width=10:1, names=head(letters, 10)),
                  Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
                  score=1:10, GC=seq(1, 0, length=10),
                  seqinfo=seqinfo)
    stopifnot(identical(gr0, gr))

    ## ---------------------------------------------------------------------
    ## COERCION
    ## ---------------------------------------------------------------------
    ## From GRanges:
    as.character(gr)
    as.factor(gr)
    as.data.frame(gr)

    ## From character to GRanges:
    x1 <- "chr2:56-125"
    as(x1, "GRanges")
    as(rep(x1, 4), "GRanges")
    x2 <- c(A=x1, B="chr1:25-30:-")
    as(x2, "GRanges")

    ## From data.frame to GRanges:
    df <- data.frame(chrom="chr2", start=11:15, end=20:24)
    gr3 <- as(df, "GRanges")

    ## Alternatively, coercion to GRanges can be done by just calling the
    ## GRanges() constructor on the object to coerce:
    gr1 <- GRanges(x1)  # same as as(x1, "GRanges")
    gr2 <- GRanges(x2)  # same as as(x2, "GRanges")
    gr3 <- GRanges(df)  # same as as(df, "GRanges")

    ## Sanity checks:
    stopifnot(identical(as(x1, "GRanges"), gr1))
    stopifnot(identical(as(x2, "GRanges"), gr2))
    stopifnot(identical(as(df, "GRanges"), gr3))

    ## ---------------------------------------------------------------------
    ## SUMMARIZING ELEMENTS
    ## ---------------------------------------------------------------------
    table(seqnames(gr))
    table(strand(gr))
    sum(width(gr))
    table(gr)
    summary(mcols(gr)[,"score"])

    ## The number of lines displayed in the 'show' method are controlled
    ## with two global options:
    longGR  <- sample(gr, 25, replace=TRUE)
    longGR
    options(showHeadLines=7)
    options(showTailLines=2)
    longGR

    ## Revert to default values
    options(showHeadLines=NULL)
    options(showTailLines=NULL)

    ## ---------------------------------------------------------------------
    ## INVERTING THE STRAND
    ## ---------------------------------------------------------------------
    invertStrand(gr)

    ## ---------------------------------------------------------------------
    ## RENAMING THE UNDERLYING SEQUENCES
    ## ---------------------------------------------------------------------
    seqlevels(gr)
    seqlevels(gr) <- sub("chr", "Chrom", seqlevels(gr))
    gr
    seqlevels(gr) <- sub("Chrom", "chr", seqlevels(gr)) # revert

    ## ---------------------------------------------------------------------
    ## COMBINING OBJECTS
    ## ---------------------------------------------------------------------
    gr2 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 3, 4)),
                   IRanges(1:10, width=5),
                   strand='-',
                   score=101:110, GC=runif(10),
                   seqinfo=seqinfo)
    gr3 <- GRanges(seqnames=Rle(c('chr1', 'chr2', 'chr3'), c(3, 4, 3)),
                   IRanges(101:110, width=10),
                   strand='-',
                   score=21:30,
                   seqinfo=seqinfo)
    some.gr <- c(gr, gr2)

    c(gr, gr2, gr3)
    c(gr, gr2, gr3, ignore.mcols=TRUE)

    ## ---------------------------------------------------------------------
    ## USING A GRANGES OBJECT AS A SUBSCRIPT TO SUBSET ANOTHER OBJECT
    ## ---------------------------------------------------------------------
    ## Subsetting *by* a GRanges subscript is supported only if the object
    ## to subset is a named list-like object:
    x <- RleList(chr1=101:120, chr2=2:-8, chr3=31:40)
    x[gr]

[Package GenomicRanges version 1.40.0 Index]