Seqinfo-class: Seqinfo objects
In Bioconductor/GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Seqinfo-class

R Documentation

Seqinfo objects

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

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 ('getChromInfoFromNCBI()' or '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
}

Bioconductor/GenomeInfoDb documentation built on Dec. 2, 2024, 1:41 a.m.