GRangesList-class: GRangesList objects

In GenomicRanges: Representation and manipulation of genomic intervals

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. Pag<c3><a8>s

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

Example output

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
GRangesList object of length 3:
$gr1 
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     score        GC
         <Rle> <IRanges>  <Rle> | <integer> <numeric>
  [1]     chr2       3-6      + |         5      0.45

$gr2 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]     chr1    7-9      + |     3 0.3
  [2]     chr1  13-15      - |     4 0.5

$gr3 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]     chr1    1-3      - |     6 0.4
  [2]     chr2    4-9      - |     2 0.1

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
gr1 gr2 gr3 
  1   2   2 
    chr2 chr1
gr1    1    0
gr2    0    2
gr3    1    1
GRangesList object of length 3:
$gr1 
GRanges object with 0 ranges and 2 metadata columns:
   seqnames    ranges strand |     score        GC
      <Rle> <IRanges>  <Rle> | <integer> <numeric>

$gr2 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]     chr1    7-9      + |     3 0.3
  [2]     chr1  13-15      - |     4 0.5

$gr3 
GRanges object with 1 range and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]     chr1    1-3      - |     6 0.4

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$gr1 
GRanges object with 0 ranges and 2 metadata columns:
   seqnames    ranges strand |     score        GC
      <Rle> <IRanges>  <Rle> | <integer> <numeric>

$gr2 
GRanges object with 1 range and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]     chr1    7-9      + |     3 0.3

$gr3 
GRanges object with 0 ranges and 2 metadata columns:
     seqnames ranges strand | score GC

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[1] "chr2" "chr1"
GRangesList object of length 3:
$gr1 
GRanges object with 1 range and 2 metadata columns:
      seqnames    ranges strand |     score        GC
         <Rle> <IRanges>  <Rle> | <integer> <numeric>
  [1]   Chrom2       3-6      + |         5      0.45

$gr2 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]   Chrom1    7-9      + |     3 0.3
  [2]   Chrom1  13-15      - |     4 0.5

$gr3 
GRanges object with 2 ranges and 2 metadata columns:
      seqnames ranges strand | score  GC
  [1]   Chrom1    1-3      - |     6 0.4
  [2]   Chrom2    4-9      - |     2 0.1

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
IRangesList of length 3
$gr1
IRanges object with 1 range and 2 metadata columns:
          start       end     width |     score        GC
      <integer> <integer> <integer> | <integer> <numeric>
  [1]         3         6         4 |         5      0.45

$gr2
IRanges object with 2 ranges and 2 metadata columns:
          start       end     width |     score        GC
      <integer> <integer> <integer> | <integer> <numeric>
  [1]         7         9         3 |         3       0.3
  [2]        13        15         3 |         4       0.5

$gr3
IRanges object with 2 ranges and 2 metadata columns:
          start       end     width |     score        GC
      <integer> <integer> <integer> | <integer> <numeric>
  [1]         1         3         3 |         6       0.4
  [2]         4         9         6 |         2       0.1

 gr1  gr2  gr3 
TRUE TRUE TRUE 
GRangesList object of length 3:
$gr1 
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]   Chrom2       3-6      +

$gr2 
GRanges object with 2 ranges and 0 metadata columns:
      seqnames ranges strand
  [1]   Chrom1    7-9      +
  [2]   Chrom1  13-15      -

$gr3 
GRanges object with 2 ranges and 0 metadata columns:
      seqnames ranges strand
  [1]   Chrom2    4-9      -
  [2]   Chrom1    1-3      -

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GRangesList object of length 3:
$XM_001065892.1 
GRanges object with 2 ranges and 0 metadata columns:
      seqnames              ranges strand
         <Rle>           <IRanges>  <Rle>
  [1]     chr4 124513961-124514087      +
  [2]     chr4 124514706-124515691      +

$XM_578205.2 
GRanges object with 3 ranges and 0 metadata columns:
      seqnames              ranges strand
  [1]     chr2 155875533-155876067      -
  [2]     chr2 155879894-155880030      -
  [3]     chr2 155895543-155895690      -

$NM_012543.2 
GRanges object with 4 ranges and 0 metadata columns:
      seqnames            ranges strand
  [1]     chr1 96173572-96174077      +
  [2]     chr1 96174920-96175330      +
  [3]     chr1 96176574-96176785      +
  [4]     chr1 96177991-96178484      +

-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths

GenomicRanges documentation built on Nov. 8, 2020, 5:46 p.m.