GRanges objects

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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, ..., seqlengths=NULL, seqinfo=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.

...

Optional metadata columns. These columns cannot be named "start", "end", "width", or "element".

seqlengths

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

seqinfo

NULL, or a Seqinfo object containing allowed sequence names, lengths (or NA), and circularity flag, 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").

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 a RangedData, or RangesList 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, "RangesList"): Creates a RangesList 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, "RangesList"): Turns Seqinfo object x (with no NA lengths) into a GRanges or RangesList.

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 a Ranges object.

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

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

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, force=FALSE) <- 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.mcols=FALSE): Gets a GRanges with only the range information from x, unless use.mcols is TRUE, in which case the metadata columns are also returned. Those columns will include any "extra column slots" if x is a specialized GenomicRanges derivative.

Ranges methods

In the following code snippets, x is a GRanges 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)).

Splitting and Combining

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

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.

c(x, ...): Combines x and the GRanges 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.

c(x, ..., ignore.mcols=FALSE) If the GRanges objects have metadata columns (represented as one DataFrame per object), each such DataFrame must have the same columns in order to combine successfully. In order to circumvent this restraint, you can pass in an ignore.mcols=TRUE argument which will combine all the objects into one and drop all of their metadata columns.

split(x, f, drop=FALSE): Splits 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.

Subsetting

In the code snippets below, x is a GRanges 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; or a 'logical' Rle object.

x[i, j] <- value: Replaces elements i and optional metadata columns j with value.

head(x, n = 6L): If n is non-negative, returns the first n elements of the GRanges object. If n is negative, returns all but the last abs(n) elements of the GRanges 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 elements of the GRanges object. If n is negative, returns all but the first abs(n) elements of the GRanges object.

window(x, start = NA, end = NA, width = NA, frequency = NULL, delta = NULL, ...): Extracts the subsequence window from the GRanges object using:

start, end, width

The start, end, or width of the window. Two of the three are required.

frequency, delta

Optional arguments that specify the sampling frequency and increment within the window.

In general, this is more efficient than using "[" operator.

window(x, start = NA, end = NA, width = NA, keepLength = TRUE) <- value: Replaces the subsequence window specified on the left (i.e. the subsequence in x specified by start, end and width) by value. value must either be of class class(x), belong to a subclass of class(x), be coercible to class(x), or be NULL. If keepLength is TRUE, the elements of value are repeated to create a GRanges object with the same number of elements as the width of the subsequence window it is replacing. If keepLength is FALSE, this replacement method can modify the length of x, depending on how the length of the left subsequence window compares to the length of value.

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.

Note that a GRanges object can be used to 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)])

Other methods

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

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

  • seqinfo for accessing/modifying information about the underlying sequences of a GRanges object.

  • The GPos class, a memory-efficient container for storing genomic positions, that is, genomic ranges of width 1.

  • GenomicRanges-comparison for comparing and ordering genomic ranges.

  • findOverlaps-methods for finding/counting overlapping genomic ranges.

  • intra-range-methods and inter-range-methods for intra range and inter range transformations of a GRanges object.

  • coverage-methods for computing the coverage of a GRanges object.

  • setops-methods for set operations on GRanges objects.

  • nearest-methods for finding the nearest genomic range 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.

  • Ranges objects in the IRanges package.

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

Examples

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## ---------------------------------------------------------------------
## 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)

## all.gr <- c(gr, gr2, gr3) ## (This would fail)
all.gr <- 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]