GTuplesList-class: GTuplesList objects
In PeteHaitch/GenomicTuples: Representation and Manipulation of Genomic Tuples
GTuplesList-class R Documentation
GTuplesList objects
Description
The GTuplesList class is a container for storing a collection of
GTuples objects. It is derived from
GRangesList.
Constructor
GTuplesList(...):-
Creates a GTuplesList object using GTuples objects
supplied in ....
Accessors
In the following code snippets, x is a GTuplesList
object.
length(x):-
Get the number of list elements.
names(x), names(x) <- value:-
Get or set the names on x.
elementNROWS(x):-
Get the length of each of the list elements.
isEmpty(x):-
Returns a logical indicating either if the GTuplesList 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.
tuples(x), tuples(x) <- value:-
Get or set the tuples in the form of a
SimpleList of integer matrices. value can
be a a single integer matrix.
ranges(x, use.mcols = FALSE), ranges(x) <- value:-
Get or set the ranges in the form of a
CompressedIRangesList. value can be a
IntegerRangesList object.
WARNING: The use of ranges with GTuplesList
objects is strongly discouraged. It will only get/set
pos_{1} and pos_{m} of the tuples, where m is the
size of the tuples, as these are what are stored in the "ranges"
slot of the GTuples objects.
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 GTuplesList
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.-
Tuples methods
In the following code snippets, x is a GTuplesList object.
WARNING: The preferred setter is tuples(x) <- value and the
use of start(x) <- value, end(x) <- value and
width(x) <- value is discouraged.
start(x), start(x) <- value:-
Get or set pos_{1} of the tuples. WARNING: The use
of start(x) <- value is discouraged; instead, construct the
tuples as the appropriate List of integer matrices, mvalue,
and use tuples(x) <- mvalue.
end(x), end(x) <- value:-
Get or set pos_{m} of the tuples, where m is the size
of the tuples. WARNING: The use of end(x) <- value is
discouraged; instead, construct the tuples as the appropriate List
of integer matrices, mvalue, and use tuples(x) <- mvalue.
IPD(x):-
Get the intra-pair distances (IPD) in the form of a
SimpleList of integer matrices. IPD is
only defined for tuples with size > 1. The IPD of a tuple
with size= m is the vector of intra-pair distances,
(pos_{2} - pos_{1}, \ldots, pos_{m} - pos_{m - 1}).
width(x), width(x) <- value:-
Get or set pos_{m} - pos_{1} of the tuples, where m is the
size of the tuples. If using width(x) <- value,
pos_{1} is held fixed and pos_{m} is altered.
WARNING: The use of width(x) <- value is discouraged;
instead, instead, construct the tuples as the appropriate List
of integer matrices, mvalue, and use tuples(x) <- mvalue.
Coercion
In the code snippets below, x is a GTuplesList 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, "GRangesList"):-
Creates a GRangesList object from a
GTuplesList object. WARNING: This is generally a
destructive operation, as the original GTuplesList may not
be re-creatable.
Subsetting
In the following code snippets, x is a GTuplesList 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
GTuplesList object.
If n is negative, returns all but the last abs(n) elements
of the GTuplesList object.
rep(x, times, length.out, each):-
Repeats the values in x through one of the following conventions:
timesVector 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
GTuples object.
If n is negative, returns all but the first abs(n) elements
of the GTuples object.
Combining
In the code snippets below, x is a GTuplesList object.
c(x, ...):-
Combines x and the GTuplesList 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 GTuples
object.
Looping
In the code snippets below, x is a GTuplesList 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 GTuplesList 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
GTuplesList objects.
mapply(FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE,
USE.NAMES = TRUE):-
Like the standard mapply function defined in the
base package, the mapply method for GTuplesList 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 GTuplesList objects
is a user-friendly version of lapply by default returning a vector
or matrix if appropriate.
Author(s)
Peter Hickey for GTuplesList definition and methods. P. Aboyoun
& H. Pagès for all the real work underlying the powerful GRangesList
class and methods.
See Also
GTuples-class
seqinfo,
GRangesList,
Vector,
IntegerRangesList,
RleList,
DataFrameList,
findOverlaps-methods
Examples
## Construction of GTuplesList of 4-tuples with GTuplesList():
seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
gt4 <- GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
c(1, 3, 2, 4)),
tuples = matrix(c(1:10, 2:11, 3:12, 4:13), ncol = 4),
strand = Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10, GC = seq(1, 0, length = 10), seqinfo = seqinfo)
gtl4 <- GTuplesList(A = gt4[1:4], B = gt4[5:10])
gtl4
## Summarizing elements:
elementNROWS(gtl4)
table(seqnames(gtl4))
## Extracting subsets:
gtl4[seqnames(gtl4) == "chr1", ]
gtl4[seqnames(gtl4) == "chr1" & strand(gtl4) == "+", ]
## Renaming the underlying sequences:
seqlevels(gtl4)
seqlevels(gtl4) <- sub("chr", "Chrom", seqlevels(gtl4))
gtl4
## Coerce to GRangesList ("internal positions" information is lost):
as(gtl4, "GRangesList")
## Get the size of the tuples stored in the GTuplesList object
size(gtl4)
## Get the tuples
tuples(gtl4)
## Get the matrix of intra-pair distances (IPD)
IPD(gtl4)
## Can't combine genomic tuples of different sizes
gt1 <- GTuples('chr1', matrix(30:40))
gt1
## Not run:
## Returns error
GTuplesList(A = gt4, gt1)
## End(Not run)
PeteHaitch/GenomicTuples documentation built on Nov. 5, 2024, 2 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| GTuplesList-class | R Documentation |
GTuplesList objects
Description
The GTuplesList class is a container for storing a collection of
GTuples objects. It is derived from
GRangesList.
Constructor
GTuplesList(...):-
Creates a
GTuplesListobject usingGTuplesobjects supplied in....
Accessors
In the following code snippets, x is a GTuplesList
object.
length(x):-
Get the number of list elements.
names(x),names(x) <- value:-
Get or set the names on
x. elementNROWS(x):-
Get the
lengthof each of the list elements. isEmpty(x):-
Returns a logical indicating either if the
GTuplesListhas 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.valuecan be anRleListorCharacterListobject. tuples(x),tuples(x) <- value:-
Get or set the tuples in the form of a
SimpleListof integer matrices.valuecan be a a single integer matrix. ranges(x, use.mcols = FALSE),ranges(x) <- value:-
Get or set the ranges in the form of a
CompressedIRangesList.valuecan be aIntegerRangesListobject.WARNING: The use of
rangeswithGTuplesListobjects is strongly discouraged. It will only get/setpos_{1}andpos_{m}of the tuples, wheremis thesizeof the tuples, as these are what are stored in the "ranges" slot of theGTuplesobjects. strand(x),strand(x) <- value:-
Get or set the strand in the form of an
RleList.valuecan be anRleList,CharacterListor single character.valueas a single character converts all ranges inxto the samevalue; for selective strand conversion (i.e., mixed “+” and “-”) useRleListorCharacterList. mcols(x, use.names=FALSE),mcols(x) <- value:-
Get or set the metadata columns.
valuecan beNULL, or a data.frame-like object (i.e.DataFrameor data.frame) holding element-wise metadata. elementMetadata(x),elementMetadata(x) <- value,values(x),values(x) <- value:-
Alternatives to
mcolsfunctions. Their use is discouraged. seqinfo(x),seqinfo(x) <- value:-
Get or set the information about the underlying sequences.
valuemust be a Seqinfo object. seqlevels(x),seqlevels(x, force=FALSE) <- value:-
Get or set the sequence levels.
seqlevels(x)is equivalent toseqlevels(seqinfo(x))or tolevels(seqnames(x)), those 2 expressions being guaranteed to return identical character vectors on aGTuplesListobject.valuemust be a character vector with no NAs. See?seqlevelsfor more information. seqlengths(x),seqlengths(x) <- value:-
Get or set the sequence lengths.
seqlengths(x)is equivalent toseqlengths(seqinfo(x)).valuecan 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 toisCircular(seqinfo(x)).valuemust 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 togenome(seqinfo(x)).valuemust 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.
Tuples methods
In the following code snippets, x is a GTuplesList object.
WARNING: The preferred setter is tuples(x) <- value and the
use of start(x) <- value, end(x) <- value and
width(x) <- value is discouraged.
start(x),start(x) <- value:-
Get or set
pos_{1}of thetuples. WARNING: The use ofstart(x) <- valueis discouraged; instead, construct the tuples as the appropriateListof integer matrices,mvalue, and usetuples(x) <- mvalue. end(x),end(x) <- value:-
Get or set
pos_{m}of the tuples, wheremis thesizeof the tuples. WARNING: The use ofend(x) <- valueis discouraged; instead, construct the tuples as the appropriateListof integer matrices,mvalue, and usetuples(x) <- mvalue. IPD(x):-
Get the intra-pair distances (
IPD) in the form of aSimpleListof integer matrices.IPDis only defined for tuples withsize> 1. TheIPDof a tuple withsize= mis the vector of intra-pair distances,(pos_{2} - pos_{1}, \ldots, pos_{m} - pos_{m - 1}). width(x),width(x) <- value:-
Get or set
pos_{m} - pos_{1}of the tuples, wheremis thesizeof the tuples. If usingwidth(x) <- value,pos_{1}is held fixed andpos_{m}is altered. WARNING: The use ofwidth(x) <- valueis discouraged; instead, instead, construct the tuples as the appropriateListof integer matrices,mvalue, and usetuples(x) <- mvalue.
Coercion
In the code snippets below, x is a GTuplesList object.
as.data.frame(x, row.names = NULL, optional = FALSE, ..., value.name = "value", use.outer.mcols = FALSE, group_name.as.factor = FALSE):-
Coerces
xto adata.frame. See as.data.frame on theListman page for details (?List). as.list(x, use.names = TRUE):-
Creates a list containing the elements of
x.
as(x, "GRangesList"):-
Creates a
GRangesListobject from aGTuplesListobject. WARNING: This is generally a destructive operation, as the originalGTuplesListmay not be re-creatable.
Subsetting
In the following code snippets, x is a GTuplesList object.
x[i, j],x[i, j] <- value:-
Get or set elements
iwith optional metadata columnsmcols(x)[,j], whereican 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, whereiis a numeric or character vector of length 1. x$name,x$name <- value:-
Get or set element
name, wherenameis a name or character vector of length 1. head(x, n = 6L):-
If
nis non-negative, returns the first n elements of the GTuplesList object. Ifnis negative, returns all but the lastabs(n)elements of the GTuplesList object. rep(x, times, length.out, each):-
Repeats the values in
xthrough one of the following conventions:timesVector 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
xis repeatedeachtimes.
subset(x, subset):-
Returns a new object of the same class as
xmade of the subset using logical vectorsubset, where missing values are taken asFALSE. tail(x, n = 6L):-
If
nis non-negative, returns the last n elements of the GTuples object. Ifnis negative, returns all but the firstabs(n)elements of the GTuples object.
Combining
In the code snippets below, x is a GTuplesList object.
c(x, ...):-
Combines
xand the GTuplesList objects in...together. Any object in...must belong to the same class asx, or to one of its subclasses, or must beNULL. The result is an object of the same class asx. append(x, values, after = length(x)):-
Inserts the
valuesintoxat the position given byafter, wherexandvaluesare of the same class. unlist(x, recursive = TRUE, use.names = TRUE):-
Concatenates the elements of
xinto a single GTuples object.
Looping
In the code snippets below, x is a GTuplesList object.
endoapply(X, FUN, ...):-
Similar to
lapply, but performs an endomorphism, i.e. returns an object ofclass(X). lapply(X, FUN, ...):-
Like the standard
lapplyfunction defined in the base package, thelapplymethod for GTuplesList objects returns a list of the same length asX, with each element being the result of applyingFUNto the corresponding element ofX. Map(f, ...):-
Applies a function to the corresponding elements of given GTuplesList objects.
mapply(FUN, ..., MoreArgs = NULL, SIMPLIFY = TRUE, USE.NAMES = TRUE):-
Like the standard
mapplyfunction defined in the base package, themapplymethod for GTuplesList objects is a multivariate version ofsapply. mendoapply(FUN, ..., MoreArgs = NULL):-
Similar to
mapply, but performs an endomorphism across multiple objects, i.e. returns an object ofclass(list(...)[[1]]). Reduce(f, x, init, right = FALSE, accumulate = FALSE):-
Uses a binary function to successively combine the elements of
xand 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
sapplyfunction defined in the base package, thesapplymethod for GTuplesList objects is a user-friendly version oflapplyby default returning a vector or matrix if appropriate.
Author(s)
Peter Hickey for GTuplesList definition and methods. P. Aboyoun
& H. Pagès for all the real work underlying the powerful GRangesList
class and methods.
See Also
GTuples-class
seqinfo,
GRangesList,
Vector,
IntegerRangesList,
RleList,
DataFrameList,
findOverlaps-methods
Examples
## Construction of GTuplesList of 4-tuples with GTuplesList():
seqinfo <- Seqinfo(paste0("chr", 1:3), c(1000, 2000, 1500), NA, "mock1")
gt4 <- GTuples(seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"),
c(1, 3, 2, 4)),
tuples = matrix(c(1:10, 2:11, 3:12, 4:13), ncol = 4),
strand = Rle(strand(c("-", "+", "*", "+", "-")),
c(1, 2, 2, 3, 2)),
score = 1:10, GC = seq(1, 0, length = 10), seqinfo = seqinfo)
gtl4 <- GTuplesList(A = gt4[1:4], B = gt4[5:10])
gtl4
## Summarizing elements:
elementNROWS(gtl4)
table(seqnames(gtl4))
## Extracting subsets:
gtl4[seqnames(gtl4) == "chr1", ]
gtl4[seqnames(gtl4) == "chr1" & strand(gtl4) == "+", ]
## Renaming the underlying sequences:
seqlevels(gtl4)
seqlevels(gtl4) <- sub("chr", "Chrom", seqlevels(gtl4))
gtl4
## Coerce to GRangesList ("internal positions" information is lost):
as(gtl4, "GRangesList")
## Get the size of the tuples stored in the GTuplesList object
size(gtl4)
## Get the tuples
tuples(gtl4)
## Get the matrix of intra-pair distances (IPD)
IPD(gtl4)
## Can't combine genomic tuples of different sizes
gt1 <- GTuples('chr1', matrix(30:40))
gt1
## Not run:
## Returns error
GTuplesList(A = gt4, gt1)
## End(Not run)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.