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Last data update: 2014.03.03

R: GRangesList objects

GRangesList-class

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.

Accessors

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

: length(x): Get the number of list elements.
: names(x), names(x) <- value: Get or set the names on x.
: 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.
: 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 a RangesList 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. 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.
: 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.
: 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.
: as(from, "GRangesList"): Creates a GRangesList object from a RangedDataList 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.

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.

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><83><c2><a8>s

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:
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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenomicRanges)
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicRanges/GRangesList-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GRangesList-class
> ### Title: GRangesList objects
> ### Aliases: class:GRangesList GRangesList-class GRangesList GRangesList
> ###   makeGRangesListFromFeatureFragments updateObject,GRangesList-method
> ###   seqnames,GRangesList-method seqnames<-,GRangesList-method
> ###   ranges,GRangesList-method ranges<-,GRangesList-method
> ###   start,GRangesList-method start<-,GRangesList-method
> ###   end,GRangesList-method end<-,GRangesList-method
> ###   width,GRangesList-method width<-,GRangesList-method
> ###   strand,GRangesList-method strand<-,GRangesList,ANY-method
> ###   strand<-,GRangesList,character-method
> ###   elementMetadata,GRangesList-method
> ###   elementMetadata<-,GRangesList-method seqinfo,GRangesList-method
> ###   seqinfo<-,GRangesList-method score,GRangesList-method
> ###   score<-,GRangesList-method
> ###   coerce,GRangesList,CompressedIRangesList-method
> ###   coerce,GRangesList,IRangesList-method
> ###   coerce,GRangesList,RangesList-method
> ###   coerce,GRanges,GRangesList-method
> ###   coerce,RangedDataList,GRangesList-method [,GRangesList,ANY-method
> ###   [<-,GRangesList-method [<-,GRangesList,ANY-method
> ###   [<-,GRangesList,ANY,ANY,ANY-method [[<-,GRangesList-method
> ###   [[<-,GRangesList,ANY-method [[<-,GRangesList,ANY,ANY-method
> ###   relistToClass,GRanges-method show,GRangesList-method
> 
> ### ** 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
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
> 
> ## Summarizing elements:
> elementNROWS(grl)
gr1 gr2 gr3 
  1   2   2 
> table(seqnames(grl))
    chr2 chr1
gr1    1    0
gr2    0    2
gr3    1    1
> 
> ## Extracting subsets:
> grl[seqnames(grl) == "chr1", ]
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
> grl[seqnames(grl) == "chr1" & strand(grl) == "+", ]
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
> 
> ## Renaming the underlying sequences:
> seqlevels(grl)
[1] "chr2" "chr1"
> seqlevels(grl) <- sub("chr", "Chrom", seqlevels(grl))
> grl
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
> 
> ## Coerce to IRangesList (seqnames and strand information is lost):
> as(grl, "IRangesList")
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

> 
> ## isDisjoint():
> isDisjoint(grl)
 gr1  gr2  gr3 
TRUE TRUE TRUE 
> 
> ## disjoin():
> disjoin(grl)  # metadata columns and order NOT preserved
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
> 
> ## 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
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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

GRangesList objects

Description

Constructors

Accessors

Coercion

Subsetting

Combining

Looping

Author(s)

See Also

Examples

Results