Package 'Seqinfo'

Description

A GenomeDescription object holds the meta information describing a given genome.

Constructor

Even though a constructor function is provided (GenomeDescription()), it is rarely needed GenomeDescription objects are typically obtained by coercing a BSgenome object to GenomeDescription. This has the effect of stripping the sequences from the object and retaining only the meta information that describes the genome. See the Examples section below for an example.

Accessor methods

In the code snippets below, object or x is a GenomeDescription object.

organism(object):

Return the scientific name of the organism of the genome e.g. "Homo sapiens", "Mus musculus", "Caenorhabditis elegans", etc...

commonName(object):

Return the common name of the organism of the genome e.g. "Human", "Mouse", "Worm", etc...

providerVersion(x):

Return the name of the genome. This is typically the name of an NCBI assembly (e.g. GRCh38.p13, WBcel235, TAIR10.1, ARS-UCD1.2, etc...) or UCSC genome (e.g. hg38, bosTau9, galGal6, ce11, etc...).

provider(x):

Return the provider of this genome e.g. "UCSC", "BDGP", "FlyBase", etc...

releaseDate(x):

Return the release date of this genome e.g. "Mar. 2006".

bsgenomeName(x):

Uses the meta information stored in GenomeDescription object x to construct the name of the corresponding BSgenome data package (see the available.genomes function in the BSgenome package for details about the naming scheme used for those packages). Note that there is no guarantee that a package with that name actually exists.

seqinfo(x)

Gets information about the genome sequences. This information is returned in a Seqinfo object. Each part of the information can be retrieved separately with seqnames(x), seqlengths(x), and isCircular(x), respectively, as described below.

seqnames(x)

Gets the names of the genome sequences. seqnames(x) is equivalent to seqnames(seqinfo(x)).

seqlengths(x)

Gets the lengths of the genome sequences. seqlengths(x) is equivalent to seqlengths(seqinfo(x)).

isCircular(x)

Returns the circularity flags of the genome sequences. isCircular(x) is equivalent to isCircular(seqinfo(x)).

Author(s)

H. Pagès

See Also

• The available.genomes function and the BSgenome class in the BSgenome package.

• The Seqinfo class.

Examples

library(BSgenome.Celegans.UCSC.ce2)
BSgenome.Celegans.UCSC.ce2
as(BSgenome.Celegans.UCSC.ce2, "GenomeDescription")

Description

rankSeqlevels assigns a unique ID to each unique sequence name in the input vector. The returned IDs span 1:N where N is the number of unique sequence names in the input vector.

orderSeqlevels is similar to rankSeqlevels except that the returned vector contains the order instead of the rank.

Usage

rankSeqlevels(seqnames, X.is.sexchrom=NA)
orderSeqlevels(seqnames, X.is.sexchrom=NA)

Arguments

Value

An integer vector of the same length as seqnames that tries to reflect the “natural” order of seqnames, e.g.,chr1, chr2, chr3, ...

The values in the returned vector span 1:N where N is the number of unique sequence names in the input vector.

Author(s)

H. Pagès for rankSeqlevels, orderSeqlevels added by Sonali Arora

See Also

• sortSeqlevels for sorting the sequence levels of an object in "natural" order.

Examples

si <- Seqinfo(genome="sacCer2")
rankSeqlevels(seqnames(si))
rankSeqlevels(seqnames(si)[c(1:5,5:1)])

newchr <- paste0("chr",c(1:3,6:15,4:5,16:22))
newchr
orderSeqlevels(newchr)
rankSeqlevels(newchr)

Description

A set of generic functions for getting/setting/modifying the sequence information stored in an object.

Usage

seqinfo(x)
seqinfo(x,
        new2old=NULL,
        pruning.mode=c("error", "coarse", "fine", "tidy")) <- value

seqnames(x)
seqnames(x) <- value

seqlevels(x)
seqlevels(x,
          pruning.mode=c("error", "coarse", "fine", "tidy")) <- value
seqlevels0(x)
restoreSeqlevels(x)

seqlengths(x)
seqlengths(x) <- value

isCircular(x)
isCircular(x) <- value

genome(x)
genome(x) <- value

Arguments

    seqlevels(x) <- seqlevels(value)  # align seqlevels
    seqinfo(x) <- seqinfo(value)  # guaranteed to work
    

    seqlevels(x, pruning.mode="coarse") <- seqlevels(value)
    seqinfo(x) <- seqinfo(value)  # guaranteed to work
    

Details

"It all revolves around Seqinfo objects"

The Seqinfo class plays a central role for the functions described in this man page because:

1. All these functions (except seqinfo, seqlevels0, and restoreSeqlevels) work on a Seqinfo object.

2. For classes that implement it, the seqinfo getter should return a Seqinfo object.

3. Default seqlevels, seqlengths, isCircular, and genome getters and setters are provided. By default, seqlevels(x) does seqlevels(seqinfo(x)), seqlengths(x) does seqlengths(seqinfo(x)), isCircular(x) does isCircular(seqinfo(x)), and genome(x) does genome(seqinfo(x)). So any class with a seqinfo getter will have all the above getters work out-of-the-box. If, in addition, the class defines a seqinfo setter, then all the corresponding setters will also work out-of-the-box.

   Examples of containers that have a seqinfo getter and setter:

   • the GRanges and GRangesList classes in the GenomicRanges package;

   • the SummarizedExperiment class in the SummarizedExperiment package;

   • the GAlignments, GAlignmentPairs, and GAlignmentsList classes in the GenomicAlignments package;

   • the TxDb class in the GenomicFeatures package;

   • the BSgenome class in the BSgenome package;

   • and more...

Value

The seqinfo() getter returns a Seqinfo object.

The seqnames(), seqlevels(), and seqlevels0() getters return a character vector with no NAs.

restoreSeqlevels() returns input object x with its original seqlevels restored i.e. reset to seqlevels0(x).

The seqlengths() getter returns a named integer vector, possibly with NAs.

The isCircular() getter returns a named logical vector, possibly with NAs.

The genome() getter returns a named character vector, possibly with NAs.

Note

The full list of methods defined for a given generic function can be seen with e.g. showMethods("seqinfo") or showMethods("seqnames") (for the getters), and showMethods("seqinfo<-") or showMethods("seqnames<-") (for the setters a.k.a. replacement methods). Please be aware that this shows only methods defined in packages that are currently attached.

The GenomicRanges package defines seqinfo and seqinfo<- methods for these low-level data types: List and IntegerRangesList. Those objects do not have the means to formally store sequence information. Thus, the wrappers simply store the Seqinfo object within metadata(x). Initially, the metadata is empty, so there is some effort to generate a reasonable default Seqinfo. The names of any List are taken as the seqnames, and the universe of IntegerRangesList is taken as the genome.

Author(s)

H. Pagès

See Also

• The seqlevelsStyle generic getter and setter in the GenomeInfoDb package for conveniently renaming the seqlevels of an object according to a particular naming convention (e.g. NCBI or UCSC).

• Seqinfo objects.

• GRanges and GRangesList objects in the GenomicRanges package.

• SummarizedExperiment objects in the SummarizedExperiment package.

• GAlignments, GAlignmentPairs, and GAlignmentsList objects in the GenomicAlignments package.

• TxDb objects in the GenomicFeatures package.

• BSgenome objects in the BSgenome package.

• sortSeqlevels for sorting the sequence levels of an object in "natural" order.

• seqlevelsInUse for getting the sequence levels that are used by an object.

• seqlevels-wrappers in the GenomeInfoDb package for convenience wrappers to the seqlevels getter and setter.

Examples

## ---------------------------------------------------------------------
## A. BASIC USAGE OF THE seqlevels() GETTER AND SETTER
## ---------------------------------------------------------------------
## Operations between 2 or more objects containing genomic ranges (e.g.
## finding overlaps, comparing, or matching) only make sense if the
## operands have the same seqlevels. So before performing such
## operations, it is often necessary to adjust the seqlevels in
## the operands so that they all have the same seqlevels. This is
## typically done with the seqlevels() setter. The setter can be used
## to rename, drop, add and/or reorder seqlevels of an object. The
## examples below show how to mofify the seqlevels of a GRanges object
## but the same would apply to any object containing sequence
## information (i.e. with a seqinfo() component).
library(GenomicRanges)

gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))

## Add new seqlevels:
seqlevels(gr) <- c("chr1", seqlevels(gr), "chr4")
seqlevels(gr)

## Reorder existing seqlevels:
seqlevels(gr) <- rev(seqlevels(gr))
seqlevels(gr)

## Drop some seqlevels in use:
seqlevels(gr, pruning.mode="coarse") <- setdiff(seqlevels(gr), "chr3")
gr

## Rename, add, and reorder the seqlevels all at once:
seqlevels(gr) <- c("chr1", chr2="chr2", chrM="Mitochondrion")
seqlevels(gr)

## ---------------------------------------------------------------------
## B. DROP SEQLEVELS FROM A LIST-LIKE OBJECT
## ---------------------------------------------------------------------

grl0 <- GRangesList(A=GRanges("chr2", IRanges(3:2, 5)),
                    B=GRanges(c("chr2", "chrMT"), IRanges(7:6, 15)),
                    C=GRanges(c("chrY", "chrMT"), IRanges(17:16, 25)),
                    D=GRanges())
grl0

grl1 <- grl0
seqlevels(grl1, pruning.mode="coarse") <- c("chr2", "chr5")
grl1  # grl0[[2]] was fully removed! (even if it had a range on chr2)

## If what is desired is to remove the 2nd range in grl0[[2]] only (i.e.
## the chrMT:6-15 range), or, more generally speaking, to remove the
## ranges within each list element that are located on the seqlevels to
## drop, then use pruning.mode="fine" or pruning.mode="tidy":
grl2 <- grl0
seqlevels(grl2, pruning.mode="fine") <- c("chr2", "chr5")
grl2  # grl0[[2]] not removed, but chrMT:6-15 range removed from it

## Like pruning.mode="fine" but also removes grl0[[3]].
grl3 <- grl0
seqlevels(grl3, pruning.mode="tidy") <- c("chr2", "chr5")
grl3

library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
## Pruning mode "coarse" is particularly well suited on a GRangesList
## object that contains exons grouped by transcript:
ex_by_tx <- exonsBy(txdb, by="tx")
seqlevels(ex_by_tx)
seqlevels(ex_by_tx, pruning.mode="coarse") <- "chr2L"
seqlevels(ex_by_tx)
## Pruning mode "tidy" is particularly well suited on a GRangesList
## object that contains transcripts grouped by gene:
tx_by_gene <- transcriptsBy(txdb, by="gene")
seqlevels(tx_by_gene)
seqlevels(tx_by_gene, pruning.mode="tidy") <- "chr2L"
seqlevels(tx_by_gene)

## ---------------------------------------------------------------------
## C. RENAME THE SEQLEVELS OF A TxDb OBJECT
## ---------------------------------------------------------------------

library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
seqlevels(txdb)

seqlevels(txdb) <- sub("chr", "", seqlevels(txdb))
seqlevels(txdb)

seqlevels(txdb) <- paste0("CH", seqlevels(txdb))
seqlevels(txdb)

seqlevels(txdb)[seqlevels(txdb) == "CHM"] <- "M"
seqlevels(txdb)

## Restore original seqlevels:
txdb <- restoreSeqlevels(txdb)  # same as
                                # seqlevels(txdb) <- seqlevels0(txdb)
seqlevels(txdb)

## Note that seqlevels0() and restoreSeqlevels() only work on TxDb
## objects at the moment.

## ---------------------------------------------------------------------
## D. SUBSET OBJECTS BY SEQLEVELS
## ---------------------------------------------------------------------

tx <- transcripts(txdb)
seqlevels(tx)

## Drop 'M', keep all others.
seqlevels(tx, pruning.mode="coarse") <- seqlevels(tx)[seqlevels(tx) != "M"]
seqlevels(tx)

## Drop all except 'ch3L' and 'ch3R'.
seqlevels(tx, pruning.mode="coarse") <- c("ch3L", "ch3R")
seqlevels(tx)

## ---------------------------------------------------------------------
## E. FINDING METHODS
## ---------------------------------------------------------------------

showMethods("seqinfo")
showMethods("seqinfo<-")

showMethods("seqnames")
showMethods("seqnames<-")

showMethods("seqlevels")
showMethods("seqlevels<-")

if (interactive()) {
  library(GenomicRanges)
  ?`GRanges-class`
}

Description

A Seqinfo object is used to store basic information about a set of genomic sequences, typically chromosomes (but not necessarily).

Details

A Seqinfo object has one entry per sequence. Each entry contains the following information about the sequence:

• The sequence name (a.k.a. the seqlevel) e.g. "chr1".

• The sequence length.

• The sequence circularity flag. This is a logical indicating whether the sequence is circular (TRUE) or linear (FALSE).

• Which genome the sequence belongs to e.g. "hg19".

All entries must contain at least the sequence name. The other information is optional. In addition, the seqnames in a given Seqinfo object must be unique, that is, the object is not allowed to have two entries with the same sequence name. In other words, the sequence name is used as the primary key of a Seqinfo object.

Note that Seqinfo objects are usually not used as standalone objects but are instead typically found inside higher level objects like GRanges or TxDb objects. These higher level objects will generally provide a seqinfo() accessor for getting/setting their Seqinfo component.

Constructor

Seqinfo(seqnames, seqlengths=NA, isCircular=NA, genome=NA):

Create a Seqinfo object and populate it with the supplied data.

One special form of calling the Seqinfo() constructor is to specify only the genome argument and set it to the name of an NCBI assembly (e.g. Seqinfo(genome="GRCh38.p13")) or UCSC genome (e.g. Seqinfo(genome="hg38")), in which case the sequence information is fetched from NCBI or UCSC. See Examples section below for some examples.

Accessor methods

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

length(x):

Return the number of sequences in x.

seqnames(x), seqnames(x) <- value:

Get/set the names of the sequences in x. Those names must be non-NA, non-empty and unique. They are also called the sequence levels or the keys of the Seqinfo object.

Note that, in general, the end user should not try to alter the sequence levels with seqnames(x) <- value. The recommended way to do this is with seqlevels(x) <- value as described below.

names(x), names(x) <- value:

Same as seqnames(x) and seqnames(x) <- value.

seqlevels(x):

Same as seqnames(x).

seqlevels(x) <- value:

Can be used to rename, drop, add and/or reorder the sequence levels. value must be either a named or unnamed character vector. When value has names, the names only serve the purpose of mapping the new sequence levels to the old ones. Otherwise (i.e. when value is unnamed) this mapping is implicitly inferred from the following rules:

(1) If the number of new and old levels are the same, and if the positional mapping between the new and old levels shows that some or all of the levels are being renamed, and if the levels that are being renamed are renamed with levels that didn't exist before (i.e. are not present in the old levels), then seqlevels(x) <- value will just rename the sequence levels. Note that in that case the result is the same as with seqnames(x) <- value but it's still recommended to use seqlevels(x) <- value as it is safer.

(2) Otherwise (i.e. if the conditions for (1) are not satisfied) seqlevels(x) <- value will consider that the sequence levels are not being renamed and will just perform x <- x[value].

See below for some examples.

seqlengths(x), seqlengths(x) <- value:

Get/set the length for each sequence in x.

isCircular(x), isCircular(x) <- value:

Get/set the circularity flag for each sequence in x.

genome(x), genome(x) <- value:

Get/set the genome identifier or assembly name for each sequence in x.

Subsetting

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

x[i]:

A Seqinfo object can be subsetted only by name i.e. i must be a character vector. This is a convenient way to drop/add/reorder the entries in a Seqinfo object.

See below for some examples.

Coercion

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

as.data.frame(x):

Turns x into a data frame.

Combining Seqinfo objects

Note that we provide no c() or rbind() methods for Seqinfo objects. Here is why:

c() (like rbind()) is expected to follow an "appending semantic", that is, c(x, y) is expected to form a new object by appending the entries in y to the entries in x, thus resulting in an object with length(x) + length(y) entries. The problem with such operation is that it won't be very useful in general, because it will tend to break the constraint that the seqnames of a Seqinfo object must be unique (primary key).

So instead, a merge() method is provided, with a more useful semantic. merge(x, y) does the following:

• If an entry in Seqinfo object x has the same seqname as an entry in Seqinfo object y, then the 2 entries are fusioned together to produce a single entry in the result. This fusion only happens if the 2 entries contain compatible information.

• If 2 entries cannot be fusioned because they contain incompatible information (e.g. different seqlengths or different circularity flags), then merge(x, y) fails with an informative error of why x and y could not be merged.

We also implement an update() method for Seqinfo objects.

See below for the details.

In the code snippet below, x, y, object, and value, are Seqinfo objects.

merge(x, y, ...):

Merge x and y into a single Seqinfo object where the keys (i.e. the seqnames) are union(seqnames(x), seqnames(y)). If an entry in y has the same key as an entry in x, and if the two entries contain compatible information (NA values are treated as wildcards i.e. they're compatible with anything), then the two entries are merged into a single entry in the result. If they cannot be merged (because they contain different seqlengths, and/or circularity flags, and/or genome identifiers), then an error is raised. In addition to check for incompatible sequence information, merge(x, y) also compares seqnames(x) with seqnames(y) and issues a warning if each of them has names not in the other. The purpose of these checks is to try to detect situations where the user might be combining or comparing objects that use different underlying genomes.

Note that merge() can take more than two Seqinfo objects, in which case the objects are merged from left to right e.g.

    merge(x1, x2, x3, x4)

is equivalent to

    merge(merge(merge(x1, x2), x3), x4)

intersect(x, y):

Finds the intersection between two Seqinfo objects by merging them and subsetting for the intersection of their sequence names. This makes it easy to avoid warnings about each objects not being a subset of the other one during overlap operations.

update(object, value):

Update the entries in Seqinfo object object with the corresponding entries in Seqinfo object value. Note that the seqnames in value must be a subset of the seqnames in object.

A convenience wrapper, checkCompatibleSeqinfo(), is provided for checking whether 2 objects have compatible Seqinfo components or not. checkCompatibleSeqinfo(x, y) is equivalent to merge(seqinfo(x), seqinfo(y)) so will work on any objects x and y that support seqinfo().

Author(s)

H. Pagès

See Also

• The seqinfo getter and setter.

• The getChromInfoFromNCBI and getChromInfoFromUCSC utility functions in the GenomeInfoDb package that are used behind the scene to generate a Seqinfo object for a given assembly/genome (see examples below).

Examples

## ---------------------------------------------------------------------
## A. MAKING A Seqinfo OBJECT FOR A GIVEN NCBI ASSEMBLY OR UCSC GENOME
## ---------------------------------------------------------------------

## One special form of calling the 'Seqinfo()' constructor is to specify
## only the 'genome' argument and set it to the name of an NCBI assembly
## or UCSC genome, in which case the sequence information is fetched
## from NCBI or UCSC ('GenomeInfoDb::getChromInfoFromNCBI()' or
## 'GenomeInfoDb::getChromInfoFromUCSC()' are used behind the scene
## for this so internet access is required).

if (interactive()) {
  ## NCBI assemblies (see '?registered_NCBI_assemblies' for the list of
  ## NCBI assemblies that are currently supported):
  Seqinfo(genome="GRCh38")
  Seqinfo(genome="GRCh38.p13")
  Seqinfo(genome="Amel_HAv3.1")
  Seqinfo(genome="WBcel235")
  Seqinfo(genome="TAIR10.1")

  ## UCSC genomes (see '?registered_UCSC_genomes' for the list of UCSC
  ## genomes that are currently supported):
  Seqinfo(genome="hg38")
  Seqinfo(genome="mm10")
  Seqinfo(genome="rn6")
  Seqinfo(genome="bosTau9")
  Seqinfo(genome="canFam3")
  Seqinfo(genome="musFur1")
  Seqinfo(genome="galGal6")
  Seqinfo(genome="dm6")
  Seqinfo(genome="ce11")
  Seqinfo(genome="sacCer3")
}

## ---------------------------------------------------------------------
## B. BASIC MANIPULATION OF A Seqinfo OBJECT
## ---------------------------------------------------------------------

## Note that all the arguments (except 'genome') must have the
## same length. 'genome' can be of length 1, whatever the lengths
## of the other arguments are.
x <- Seqinfo(seqnames=c("chr1", "chr2", "chr3", "chrM"),
             seqlengths=c(100, 200, NA, 15),
             isCircular=c(NA, FALSE, FALSE, TRUE),
             genome="sasquatch")
x

## Accessors:
length(x)
seqnames(x)
names(x)
seqlevels(x)
seqlengths(x)
isCircular(x)
genome(x)

## Get a compact summary:
summary(x)

## Subset by names:
x[c("chrY", "chr3", "chr1")]

## Rename, drop, add and/or reorder the sequence levels:
xx <- x
seqlevels(xx) <- sub("chr", "ch", seqlevels(xx))  # rename
xx
seqlevels(xx) <- rev(seqlevels(xx))  # reorder
xx
seqlevels(xx) <- c("ch1", "ch2", "chY")  # drop/add/reorder
xx
seqlevels(xx) <- c(chY="Y", ch1="1", "22")  # rename/reorder/drop/add
xx

## ---------------------------------------------------------------------
## C. COMBINING 2 Seqinfo OBJECTS
## ---------------------------------------------------------------------

y <- Seqinfo(seqnames=c("chr3", "chr4", "chrM"),
             seqlengths=c(300, NA, 15))
y

## ------ merge() ------

## This issues a warning:
merge(x, y)  # the entries for chr3 and chrM contain information merged
             # from the corresponding entries in 'x' and 'y'

## To get rid of the above warning, either use suppressWarnings() or
## set the genome on 'y':
suppressWarnings(merge(x, y))
genome(y) <- genome(x)
merge(x, y)

## Note that, strictly speaking, merging 2 Seqinfo objects is not
## a commutative operation:
merge(y, x)

## More precisely: In general, 'z1 <- merge(x, y)' is not identical
## to 'z2 <- merge(y, x)'. However 'z1' and 'z2' are guaranteed to
## contain the same information but with their entries possibly in
## different order.

## This contradicts what 'x' says about circularity of chr3 and chrM:
yy <- y
isCircular(yy)[c("chr3", "chrM")] <- c(TRUE, FALSE)

## We say that 'x' and 'yy' are incompatible Seqinfo objects.
yy
if (interactive()) {
  merge(x, yy)  # raises an error
}

## Sanity checks:
stopifnot(identical(x, merge(x, Seqinfo())))
stopifnot(identical(x, merge(Seqinfo(), x)))
stopifnot(identical(x, merge(x, x)))

## ------ update() ------

z <- Seqinfo(seqnames=c("chrM", "chr2", "chr3"),
             seqlengths=c(25, NA, 300),
             genome="chupacabra")
z

update(x, z)

if (interactive()) {
  update(z, x)  # not allowed
  update(x, y)  # not allowed
}

## The seqnames in the 2nd argument can always be forced to be a subset
## of the seqnames in the 1st argument with:
update(x, y[intersect(seqnames(x), seqnames(y))])  # replace entries

## Note that the above is not the same as:
merge(x, y)[seqnames(x)]                           # fusion entries

## The former is guaranteed to work, whatever the Seqinfo objects 'x'
## and 'y'. The latter requires 'x' and 'y' to be compatible.

## Sanity checks:
stopifnot(identical(x, update(x, Seqinfo())))
stopifnot(identical(x, update(x, x)))
stopifnot(identical(z, update(x, z)[seqnames(z)]))

## ---------------------------------------------------------------------
## D. checkCompatibleSeqinfo()
## ---------------------------------------------------------------------
## A simple convenience wrapper to check that 2 objects have compatible
## Seqinfo components.

library(GenomicRanges)
gr1 <- GRanges("chr3:15-25", seqinfo=x)
gr2 <- GRanges("chr3:105-115", seqinfo=y)
if (interactive()) {
  checkCompatibleSeqinfo(gr1, gr2)  # raises an error
}

Description

Get the sequence levels that are "used" by an object, that is, the sequence levels on which the object defines genomic ranges or features.

Usage

seqlevelsInUse(x)

Arguments

Value

The sequence levels in use in a character vector.

Author(s)

H. Pagès

See Also

• The seqlevels getter and setter.

• Seqinfo objects.

• GRanges and GRangesList objects in the GenomicRanges package.

Examples

library(GenomicRanges)

gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))

## Add new seqlevels:
seqlevels(gr) <- c("chr1", seqlevels(gr), "chr4")
seqlevels(gr)
seqlevelsInUse(gr)

## Drop all unused seqlevels:
seqlevels(gr) <- seqlevelsInUse(gr)

Description

A generic function and methods to sort the sequence levels of an object in "natural" order.

Usage

sortSeqlevels(x, X.is.sexchrom=NA)

Arguments

Value

The input object x with its seqlevels sorted.

Author(s)

H. Pagès

See Also

• The seqlevels getter and setter.

• rankSeqlevels, on which sortSeqlevels is based.

• Seqinfo objects.

• GRanges and GRangesList objects in the GenomicRanges package.

Examples

sortSeqlevels(c("11", "Y", "1", "10", "9", "M", "2"))

seqlevels <- c("chrXI", "chrY", "chrI", "chrX", "chrIX", "chrM", "chrII")
sortSeqlevels(seqlevels)
sortSeqlevels(seqlevels, X.is.sexchrom=TRUE)
sortSeqlevels(seqlevels, X.is.sexchrom=FALSE)

seqlevels <- c("chr2RHet", "chr4", "chrUextra", "chrYHet",
               "chrM", "chrXHet", "chr2LHet", "chrU",
               "chr3L", "chr3R", "chr2R", "chrX")
sortSeqlevels(seqlevels)

library(GenomicRanges)
gr <- GRanges()
seqlevels(gr) <- seqlevels
sortSeqlevels(gr)