seqlevels-wrappers {GenomeInfoDb} | R Documentation |
Keep, drop or rename seqlevels in objects with a Seqinfo class.
keepSeqlevels(x, value, ...) dropSeqlevels(x, value, ...) renameSeqlevels(x, value, ...) restoreSeqlevels(x, ...) keepStandardChromosomes(x, species=NULL)
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 In the case of |
species |
The species name of the Seqinfo class in which the seqlevels will be kept, dropped or renamed. |
... |
Arguments passed to other functions. |
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
function.
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.
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
replacment vector must be the same length and in the same order as the
original seqlevels(x)
.
restoreSeqlevels
: Restore the seqlevels in x
back to the
original values. Applicable only when x
is a TxDb. The
function re-initializes the TxDb which resets the seqlevels,
removes masks and any other previous modifications.
keepStandardChromosomes
:Subsetting operation that returns only the
'standard' Chromosomes. We define 'standard chromosomes' as those chromosomes
which represent sequences in the assembly that are not scaffolds. Also
referred to as 'assembly molecule' on NCBI. Applicable when x
has a Seqinfo object.This function determines which seqlevels need to be kept
using the organism's supported by GenomeInfoDb. The user can also specify the
species to get the standard Chromsomes in x
.
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 vobencha@fhcrc.org, Sonali Arora sarora@fhcrc.org
## --------------------------------------------------------------------- ## keepSeqlevels / dropSeqlevels ## --------------------------------------------------------------------- ## GRanges / GAlignments: library(GenomicRanges) gr <- GRanges(c("chr1", "chr1", "chr2", "chr3"), IRanges(1:4, width=3)) seqlevels(gr) ## Keep only 'chr1' chr1 <- keepSeqlevels(gr, "chr1") ## Drop 'chr1'. Both 'chr2' and 'chr3' are kept. chr2 <- dropSeqlevels(gr, "chr1") 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")) seqlevels(seq2) ## GRangesList / GAlignmentsList: grl <- split(gr, as.character(seqnames(gr))) dropSeqlevels(grl, c("chr1", "chr2")) galist <- split(gal, as.character(seqnames(gal))) keepSeqlevels(galist, "seq2") ## TxDb: ## A TxDb cannot be directly subset with 'keepSeqlevels' ## and 'dropSeqlevels'. library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene seqlevels(txdb) ## Not run: keepSeqlevels(txdb, "chr2L") ## fails ## End(Not run) ## GRanges or GRangesLists extracted from the TxDb can be subset. txbygene <- transcriptsBy(txdb, "gene") seqlevels(txbygene) chr2L <- keepSeqlevels(txbygene, "chr2L") seqlevels(chr2L) ## --------------------------------------------------------------------- ## renameSeqlevels ## --------------------------------------------------------------------- ## GAlignments: seqlevels(gal) ## Rename 'seq2' to 'chr2' with a named or unnamed vector. gal2a <- renameSeqlevels(gal, c(seq2="chr2")) 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")) identical(seqlevels(gal), seqlevels(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: restoreSeqlevels(txdb) seqlevels(txdb) ## End(Not run) ## --------------------------------------------------------------------- ## keepStandardChromosomes ## --------------------------------------------------------------------- gr <- GRanges(c(paste0("chr",c(1:3)), "chr1_gl000191_random", "chr1_gl000192_random"), IRanges(1:5, width=3)) gr grl <- split(gr,seqnames(gr)) ##GRanges keepStandardChromosomes(gr) ##GRangesList keepStandardChromosomes(grl) plantgr <- GRanges(c(1:5,"MT","Pltd","wrong"), IRanges(1:8,width=5)) keepStandardChromosomes(plantgr, species="Arabidopsis thaliana")