Seqinfo objects

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Description

A Seqinfo object is a table-like object that contains basic information about a set of genomic sequences. The table has 1 row per sequence and 1 column per sequence attribute. Currently the only attributes are the length, circularity flag, and genome provenance (e.g. hg19) of the sequence, but more attributes might be added in the future as the need arises.

Details

Typically Seqinfo objects are not used directly but are part of higher level objects. Those higher level objects will generally provide a seqinfo accessor for getting/setting their Seqinfo component.

Constructor

Seqinfo(seqnames, seqlengths=NA, isCircular=NA, genome=NA): Creates a Seqinfo object.

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 rows (aka the sequence levels) of 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

There are no c or rbind method for Seqinfo objects. Both would be expected to just append the rows in y to the rows in x resulting in an object of length length(x) + length(y). But that would tend to break the constraint that the seqnames of a Seqinfo object must be unique keys.

So instead, a merge method is provided.

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

merge(x, y): Merge x and y into a single Seqinfo object where the keys (aka the seqnames) are union(seqnames(x), seqnames(y)). If a row in y has the same key as a row in x, and if the 2 rows contain compatible information (NA values are compatible with anything), then they are merged into a single row 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 based on different reference genomes.

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 the objects not being subsets of each other during overlap operations.

Author(s)

H. Pag├Ęs

See Also

  • seqinfo

  • The fetchExtendedChromInfoFromUCSC utility function that is used behind the scene to make a Seqinfo object for a supported genome (see examples below).

Examples

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## ---------------------------------------------------------------------
## A. MAKING A Seqinfo OBJECT FOR A SUPPORTED GENOME
## ---------------------------------------------------------------------

if (interactive()) {
  ## This uses fetchExtendedChromInfoFromUCSC() behind the scene and
  ## thus requires internet access. See ?fetchExtendedChromInfoFromUCSC
  ## for the list of UCSC genomes that are currently supported.
  Seqinfo(genome="hg38")
  Seqinfo(genome="bosTau8")
  Seqinfo(genome="canFam3")
  Seqinfo(genome="musFur1")
  Seqinfo(genome="mm10")
  Seqinfo(genome="rn6")
  Seqinfo(genome="galGal4")
  Seqinfo(genome="dm6")
  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="toy")
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. MERGING 2 Seqinfo OBJECTS
## ---------------------------------------------------------------------

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

## This issues a warning:
merge(x, y)  # rows for chr3 and chrM are merged

## 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, i.e., 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 (i.e. the same
## rows, but typically not in the same order):
merge(y, x)

## This contradicts what 'x' says about circularity of chr3 and chrM:
isCircular(y)[c("chr3", "chrM")] <- c(TRUE, FALSE)
y
if (interactive()) {
  merge(x, y)  # raises an error
}

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