seqlevels-wrappers: Convenience wrappers to the seqlevels() getter and setter

Description

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

Usage

keepSeqlevels(x, value)
dropSeqlevels(x, value)
renameSeqlevels(x, value)
restoreSeqlevels(x)
keepStandardChromosomes(x, species=NULL)

Arguments

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).

species

The species name of the Seqinfo class in which the seqlevels will be kept, dropped or renamed.

Value

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.

Details

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.

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. 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.

Examples

Run this code


## ---------------------------------------------------------------------
## 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 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"))
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: 
# txdb <- 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")