GRangesList-class {GenomicRanges}R Documentation

GRangesList objects

Description

The GRangesList class is a container for storing a collection of GRanges objects. It is derived from GenomicRangesList.

Constructors

GRangesList(...): Creates a GRangesList object using GRanges objects supplied in ....

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.

Coercion

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

as.data.frame(x, row.names = NULL, optional = FALSE): Creates a data.frame with columns element (character), seqnames (factor), start (integer), end (integer), width (integer), strand (factor), as well as the additional metadata columns (accessed with mcols(unlist(x))).

as.list(x, use.names = TRUE): Creates a list containing the elements of x.

as(x, "IRangesList"): Turns x into an IRangesList object.

as(from, "GRangesList"): Creates a GRangesList object from a RangedDataList object.

Accessors

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

seqnames(x), seqnames(x) <- value: Get or set the sequence names in the form of an RleList. value can be an RleList or CharacterList.

ranges(x), ranges(x) <- value: Get or set the ranges in the form of a CompressedIRangesList. value can be a RangesList object.

strand(x), strand(x) <- value: Get or set the strand in the form of an RleList. value can be an RleList or CharacterList object.

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.

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 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.

seqnameStyle(x): Get or set the seqname style for x. Note that this information is not stored in x but inferred by looking up seqnames(x) against a seqname style database stored in the seqnames.db metadata package (required). seqnameStyle(x) is equivalent to seqnameStyle(seqinfo(x)) and can return more than 1 seqname style (with a warning) in case the style cannot be determined unambiguously.

score(x): Get the “score” column from the element metadata, if any.

List methods

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

length(x): Get the number of elements.

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

elementLengths(x): Get the length of each of the elements.

isEmpty(x): Returns a logical indicating either if the GRangesList has no elements or if all its elements are empty.

RangesList methods

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

shift(x, shift, use.names=TRUE): Returns a new GRangesList object containing intervals with start and end values that have been shifted by integer vector shift. The use.names argument determines whether or not to keep the names on the ranges.

isDisjoint(x) Return a vector of logical values indicating whether the ranges of each element of x are disjoint (i.e. non-overlapping).

disjoin(x, ...) Returns an object of the same type as x containing disjoint ranges calculated on each element of x.

Combining

In the code snippets below, x is a GRangesList 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 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.

unlist(x, recursive = TRUE, use.names = TRUE): Concatenates the elements of x into a single GRanges object.

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.

seqselect(x, start=NULL, end=NULL, width=NULL): Similar to window, except that multiple consecutive subsequences can be requested for concatenation. As such two of the three start, end, and width arguments can be used to specify the consecutive subsequences. Alternatively, start can take a Ranges object or something that can be converted to a Ranges object like an integer vector, logical vector or logical Rle. If the concatenation of the consecutive subsequences is undesirable, consider using Views.

seqselect(x, start=NULL, end=NULL, width=NULL) <- value: Similar to window<-, except that multiple consecutive subsequences can be replaced by a value whose length is a divisor of the number of elements it is replacing. As such two of the three start, end, and width arguments can be used to specify the consecutive subsequences. Alternatively, start can take a Ranges object or something that can be converted to a Ranges object like an integer vector, logical vector or logical Rle.

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.

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.

The "range", "reduce" and "restrict" methods

In the code snippets below, x is a GRangesList object. The methods in this section are isomorphisms, that is, they are endomorphisms (i.e. they preserve the class of x) who also preserve the length & names & metadata columns of x. In addition, the seqinfo is preserved too.

range(x): Applies range to each element in x. More precisely, it is equivalent to endoapply(x, range).

reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L): Applies reduce to each element in x. More precisely, it is equivalent to endoapply(x, reduce, drop.empty.ranges=drop.empty.ranges, min.gapwidth=min.gapwidth).

restrict(x, start = NA, end = NA, keep.all.ranges = FALSE, use.names = TRUE): Applies restrict to each element in x.

flank(x, width, start = TRUE, end = NA, keep.all.ranges = FALSE, use.names = TRUE, ignore.strand = FALSE): Applies flank to each element in x.

Author(s)

P. Aboyoun & H. Pages

See Also

GRanges-class, seqinfo, Vector-class, RangesList-class, RleList-class, DataFrameList-class, coverage-methods, setops-methods, findOverlaps-methods

Examples

## Construction with GRangesList():
gr1 <-
  GRanges(seqnames = "chr2", ranges = IRanges(3, 6),
          strand = "+", score = 5L, GC = 0.45)
gr2 <-
  GRanges(seqnames = c("chr1", "chr1"),
          ranges = IRanges(c(7,13), width = 3),
          strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
gr3 <-
  GRanges(seqnames = c("chr1", "chr2"),
          ranges = 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:
elementLengths(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

## range() and reduce():
range(grl)
reduce(grl)  # Doesn't really reduce anything but note the reordering
             # of the inner elements in the 3rd top-level element: the
             # ranges are reordered by sequence name first (the order of
             # the sequence names is dictated by the sequence levels),
             # and then by strand.
restrict(grl, start=3)
### flank
flank(grl, width =20)

## 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 1.12.1 Index]