seqinfo: Accessing/modifying sequence information

In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

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
sortSeqlevels(x, X.is.sexchrom=NA)
seqlevelsInUse(x)
seqlevels0(x)

seqlengths(x)
seqlengths(x) <- value

isCircular(x)
isCircular(x) <- value

genome(x)
genome(x) <- value

Arguments

x	The object from/on which to get/set the sequence information.
new2old	The new2old argument allows the user to rename, drop, add and/or reorder the "sequence levels" in x. new2old can be NULL or an integer vector with one element per row in Seqinfo object value (i.e. new2old and value must have the same length) describing how the "new" sequence levels should be mapped to the "old" sequence levels, that is, how the rows in value should be mapped to the rows in seqinfo(x). The values in new2old must be >= 1 and <= length(seqinfo(x)). NAs are allowed and indicate sequence levels that are being added. Old sequence levels that are not represented in new2old will be dropped, but this will fail if those levels are in use (e.g. if x is a GRanges object with ranges defined on those sequence levels) unless a pruning mode is specified via the pruning.mode argument (see below). If new2old=NULL, then sequence levels can only be added to the existing ones, that is, value must have at least as many rows as seqinfo(x) (i.e. length(values) >= length(seqinfo(x))) and also seqlevels(values)[seq_len(length(seqlevels(x)))] must be identical to seqlevels(x).
pruning.mode	When some of the seqlevels to drop from x are in use (i.e. have ranges on them), the ranges on these sequences need to be removed before the seqlevels can be dropped. We call this pruning. The pruning.mode argument controls how to prune x. Four pruning modes are currently defined: "error", "coarse", "fine", and "tidy". "error" is the default. In this mode, no pruning is done and an error is raised. The other pruning modes do the following: "coarse": Remove the elements in x where the seqlevels to drop are in use. Typically reduces the length of x. Note that if x is a list-like object (e.g. GRangesList, GAlignmentPairs, or GAlignmentsList), then any list element in x where at least one of the sequence levels to drop is in use is fully removed. In other words, when pruning.mode="coarse", the seqlevels setter will keep or remove full list elements and not try to change their content. This guarantees that the exact ranges (and their order) inside the individual list elements are preserved. This can be a desirable property when the list elements represent compound features like exons grouped by transcript (stored in a GRangesList object as returned by exonsBy( , by="tx")), or paired-end or fusion reads, etc... "fine": Supported on list-like objects only. Removes the ranges that are on the sequences to drop. This removal is done within each list element of the original object x and doesn't affect its length or the order of its list elements. In other words, the pruned object is guaranteed to be parallel to the original object. "tidy": Like the "fine" pruning above but also removes the list elements that become empty as the result of the pruning. Note that this pruning mode is particularly well suited on a GRangesList object that contains transcripts grouped by gene, as returned by transcriptsBy( , by="gene"). Finally note that, as a convenience, this pruning mode is supported on non list-like objects (e.g. GRanges or GAlignments objects) and, in this case, is equivalent to the "coarse" mode. See the "B. DROP SEQLEVELS FROM A LIST-LIKE OBJECT" section in the examples below for an extensive illustration of these pruning modes.
value	Typically a Seqinfo object for the seqinfo setter. Either a named or unnamed character vector for the seqlevels setter. A vector containing the sequence information to store for the other setters.
X.is.sexchrom	A logical indicating whether X refers to the sexual chromosome or to chromosome with Roman Numeral X. If NA, sortSeqlevels does its best to "guess".

Details

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

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

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

• 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; etc...

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.

Note

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

Author(s)

H. Pagès

See Also

• The seqlevelsStyle generic getter and setter.

• 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.

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

• rankSeqlevels, on which sortSeqlevels is based.

Examples

## Finding overlaps, comparing, and matching operations between objects
## containing genomic ranges require the objects to have the same
## seqlevels, or they fail. So before one can perform these operations,
## it is often necessary to modify the seqlevels in some of the objects
## involved in the operation so that all the objects have the same
## seqlevels. This is typically done with the seqlevels() setter. It can
## rename, drop, add and reorder seqlevels of an object. Examples below
## show how to mofify the seqlevels of GRanges, GRangesList, and TxDb
## objects but the approach is the same for any object that has seqlevels.

## ---------------------------------------------------------------------
## A. MODIFY THE SEQLEVELS OF A GRanges OBJECT
## ---------------------------------------------------------------------
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)

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

## Drop all unused seqlevels:
seqlevels(gr) <- seqlevelsInUse(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:
seqlevels(txdb) <- seqlevels0(txdb)
seqlevels(txdb)

## ---------------------------------------------------------------------
## D. SORT SEQLEVELS IN "NATURAL" ORDER
## ---------------------------------------------------------------------

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)

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

## ---------------------------------------------------------------------
## E. 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)

## ---------------------------------------------------------------------
## F. FINDING METHODS
## ---------------------------------------------------------------------

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

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

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

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

GenomeInfoDb documentation built on April 9, 2021, 6 p.m.