seqlevels-wrappers: Convenience wrappers to the seqlevels() getter and setter
In GenomeInfoDb: Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Description Usage Arguments Details Value Author(s) See Also Examples

Keep, drop or rename seqlevels in objects with a Seqinfo class.

keepSeqlevels(x, value, pruning.mode=c("error", "coarse", "fine", "tidy"))
dropSeqlevels(x, value, pruning.mode=c("error", "coarse", "fine", "tidy"))
renameSeqlevels(x, value)
restoreSeqlevels(x)
standardChromosomes(x, species=NULL)
keepStandardChromosomes(x, species=NULL,
                        pruning.mode=c("error", "coarse", "fine", "tidy"))

`x`	Any object having a Seqinfo class in which the seqlevels will be kept, dropped or renamed.
`value`	A named or unnamed character vector. Names are ignored by `keepSeqlevels` and `dropSeqlevels`. Only the values in the character vector dictate which seqlevels to keep or drop. In the case of `renameSeqlevels`, the names are used to map new sequence levels to the old (names correspond to the old levels). When `value` is unnamed, the replacement vector must the same length and in the same order as the original `seqlevels(x)`.
`pruning.mode`	See `?seqinfo` for a description of the pruning modes.
`species`	The genus and species of the organism. Supported species can be seen with `names(genomeStyles())`.

Matching and overlap operations on range objects often require that the seqlevels match before a comparison can be made (e.g., findOverlaps). keepSeqlevels, dropSeqlevels and renameSeqlevels are high-level convenience functions that wrap the low-level seqlevels setter.

keepSeqlevels, dropSeqlevels: Subsetting operations that modify the size of x. keepSeqlevels keeps only the seqlevels in value and removes all others. dropSeqlevels drops the levels in value and retains all others. If value does not match any seqlevels in x an empty object is returned.

When x is a GRangesList it is possible to have 'mixed' list elements that have ranges from different chromosomes. keepSeqlevels will not keep 'mixed' list elements
renameSeqlevels: Rename the seqlevels in x to those in value. If value is a named character vector, the names are used to map the new seqlevels to the old. When value is unnamed, the replacement vector must be the same length and in the same order as the original seqlevels(x).
restoreSeqlevels: Perform seqlevels(txdb) <- seqlevels0(txdb), that is, restore the seqlevels in x back to the original values. Applicable only when x is a TxDb object.
standardChromosomes: Lists the 'standard' chromosomes defined as sequences in the assembly that are not scaffolds; also referred to as an 'assembly molecule' in NCBI. standardChromosomes attempts to detect the seqlevel style and if more than one style is matched, e.g., 'UCSC' and 'Ensembl', the first is chosen.

x must have a Seqinfo object. species can be specified as a character string; supported species are listed with names(genomeStyles()).

When x contains seqlevels from multiple organisms all those considered standard will be kept. For example, if seqlevels are "chr1" and "chr3R" from human and fly both will be kept. If species="Homo sapiens" is specified then only "chr1" is kept.
keepStandardChromosomes: Subsetting operation that returns only the 'standard' chromosomes.

x must have a Seqinfo object. species can be specified as a character string; supported species are listed with names(genomeStyles()).

When x contains seqlevels from multiple organisms all those considered standard will be kept. For example, if seqlevels are "chr1" and "chr3R" from human and fly both will be kept. If species="Homo sapiens" is specified then only "chr1" is kept.

The x object with seqlevels removed or renamed. If x has no seqlevels (empty object) or no replacement values match the current seqlevels in x the unchanged x is returned.

Valerie Obenchain, Sonali Arora

seqinfo ## Accessing sequence information
Seqinfo ## The Seqinfo class

## ---------------------------------------------------------------------
## keepSeqlevels / dropSeqlevels 
## ---------------------------------------------------------------------

##
## GRanges / GAlignments:
##

library(GenomicRanges)
gr <- GRanges(c("chr1", "chr1", "chr2", "chr3"), IRanges(1:4, width=3))
seqlevels(gr)
## Keep only 'chr1'
gr1 <- keepSeqlevels(gr, "chr1", pruning.mode="coarse")
## Drop 'chr1'. Both 'chr2' and 'chr3' are kept.
gr2 <- dropSeqlevels(gr, "chr1", pruning.mode="coarse")

library(Rsamtools)  # for the ex1.bam file
library(GenomicAlignments)  # for readGAlignments()

fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
gal <- readGAlignments(fl)
## If 'value' is named, the names are ignored.
seq2 <- keepSeqlevels(gal, c(foo="seq2"), pruning.mode="coarse")
seqlevels(seq2)

##
## List-like objects:
##

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())
## See ?seqinfo for a description of the pruning modes.
keepSeqlevels(grl0, "chr2", pruning.mode="coarse")
keepSeqlevels(grl0, "chr2", pruning.mode="fine")
keepSeqlevels(grl0, "chr2", pruning.mode="tidy")

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)
ex_by_tx2 <- keepSeqlevels(ex_by_tx, "chr2L", pruning.mode="coarse")
seqlevels(ex_by_tx2)
## 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)
tx_by_gene2 <- keepSeqlevels(tx_by_gene, "chr2L", pruning.mode="tidy")
seqlevels(tx_by_gene2)

## ---------------------------------------------------------------------
## renameSeqlevels 
## ---------------------------------------------------------------------

##
## GAlignments:
##

seqlevels(gal)
## Rename 'seq2' to 'chr2' with a named vector.
gal2a <- renameSeqlevels(gal, c(seq2="chr2"))
## Rename 'seq2' to 'chr2' with an unnamed vector that includes all 
## seqlevels as they appear in the object.
gal2b <- renameSeqlevels(gal, c("seq1", "chr2"))
## Names that do not match existing seqlevels are ignored.
## This attempt at renaming does nothing.
gal3 <- renameSeqlevels(gal, c(foo="chr2"))
stopifnot(identical(gal, gal3))

##
## TxDb:
##

seqlevels(txdb)
## When the seqlevels of a TxDb are renamed, all future 
## extractions reflect the modified seqlevels.
renameSeqlevels(txdb, sub("chr", "CH", seqlevels(txdb)))
renameSeqlevels(txdb, c(CHM="M"))
seqlevels(txdb)

transcripts <- transcripts(txdb)
identical(seqlevels(txdb), seqlevels(transcripts))

## ---------------------------------------------------------------------
## restoreSeqlevels 
## ---------------------------------------------------------------------

## Restore seqlevels in a TxDb to original values.
## Not run: 
txdb <- restoreSeqlevels(txdb)
seqlevels(txdb)

## End(Not run)

## ---------------------------------------------------------------------
## keepStandardChromosomes
## ---------------------------------------------------------------------

##
## GRanges:
##
gr <- GRanges(c(paste0("chr",c(1:3)), "chr1_gl000191_random",
              "chr1_gl000192_random"), IRanges(1:5, width=3))
gr
keepStandardChromosomes(gr, pruning.mode="coarse")

##
## List-like objects:
##

grl <- GRangesList(GRanges("chr1", IRanges(1:2, 5)),
                   GRanges(c("chr1_GL383519v1_alt", "chr1"), IRanges(5:6, 5)))
## Use pruning.mode="coarse" to drop list elements with mixed seqlevels:
keepStandardChromosomes(grl, pruning.mode="coarse")
## Use pruning.mode="tidy" to keep all list elements with ranges on
## standard chromosomes:
keepStandardChromosomes(grl, pruning.mode="tidy")

##
## The set of standard chromosomes should not be affected by the
## particular seqlevel style currently in use:
##

## NCBI
worm <- GRanges(c("I", "II", "foo", "X", "MT"), IRanges(1:5, width=5))
keepStandardChromosomes(worm, pruning.mode="coarse")

## UCSC
seqlevelsStyle(worm) <- "UCSC"
keepStandardChromosomes(worm, pruning.mode="coarse")

## Ensembl
seqlevelsStyle(worm) <- "Ensembl"
keepStandardChromosomes(worm, pruning.mode="coarse")