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.
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.
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.
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
length(x)
, or to repeat the whole vector
if of length 1.length.out
each
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.
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.
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.
x
.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.
seqinfo
,
Vector-class,
RangesList-class,
RleList-class,
DataFrameList-class,
intra-range-methods,
inter-range-methods,
coverage-methods,
setops-methods,
findOverlaps-methods
## 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
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