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. DataFrame or data.frame) 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, "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

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 1.48.0 Index]