Last data update: 2014.03.03

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

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

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).

species

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

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.

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.

Author(s)

Valerie Obenchain vobencha@fhcrc.org, Sonali Arora

See Also

  • seqinfo ## Accessing sequence information

  • Seqinfo ## The Seqinfo class

Examples


## ---------------------------------------------------------------------
## 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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GenomeInfoDb)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomeInfoDb/seqlevels-wrappers.Rd_%03d_medium.png", width=480, height=480)
> ### Name: seqlevels-wrappers
> ### Title: Convenience wrappers to the seqlevels() getter and setter
> ### Aliases: seqlevels-wrappers keepSeqlevels dropSeqlevels renameSeqlevels
> ###   restoreSeqlevels keepStandardChromosomes
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> 
> ## ---------------------------------------------------------------------
> ## keepSeqlevels / dropSeqlevels 
> ## ---------------------------------------------------------------------
> 
> ## GRanges / GAlignments:
> 
> library(GenomicRanges)
> gr <- GRanges(c("chr1", "chr1", "chr2", "chr3"), IRanges(1:4, width=3))
> seqlevels(gr)
[1] "chr1" "chr2" "chr3"
> ## 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
Loading required package: Biostrings
Loading required package: XVector
> library(GenomicAlignments)  # for readGAlignments()
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> 
> 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)
[1] "seq2"
> 
> ## GRangesList / GAlignmentsList:
> 
> grl <- split(gr, as.character(seqnames(gr)))
> dropSeqlevels(grl, c("chr1", "chr2"))
GRangesList object of length 1:
$chr3 
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr3    [4, 6]      *

-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> galist <- split(gal, as.character(seqnames(gal)))
> keepSeqlevels(galist, "seq2")
GAlignmentsList object of length 1:
$seq2 
GAlignments object with 1789 alignments and 0 metadata columns:
         seqnames strand cigar qwidth start  end width njunc
     [1]     seq2      +   36M     36     1   36    36     0
     [2]     seq2      +   35M     35     1   35    35     0
     [3]     seq2      -   35M     35     1   35    35     0
     [4]     seq2      +   35M     35     2   36    35     0
     [5]     seq2      +   35M     35     5   39    35     0
     ...      ...    ...   ...    ...   ...  ...   ...   ...
  [1785]     seq2      +   35M     35  1524 1558    35     0
  [1786]     seq2      +   35M     35  1524 1558    35     0
  [1787]     seq2      -   35M     35  1528 1562    35     0
  [1788]     seq2      -   35M     35  1532 1566    35     0
  [1789]     seq2      -   35M     35  1533 1567    35     0

-------
seqinfo: 1 sequence from an unspecified genome
> 
> ## TxDb:
> 
> ## A TxDb cannot be directly subset with 'keepSeqlevels' 
> ## and 'dropSeqlevels'.
> library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
> txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
> seqlevels(txdb)
 [1] "chr2L"     "chr2R"     "chr3L"     "chr3R"     "chr4"      "chrX"     
 [7] "chrU"      "chrM"      "chr2LHet"  "chr2RHet"  "chr3LHet"  "chr3RHet" 
[13] "chrXHet"   "chrYHet"   "chrUextra"
> ## Not run: 
> ##D keepSeqlevels(txdb, "chr2L") ## fails
> ## End(Not run)
> 
> ## GRanges or GRangesLists extracted from the TxDb can be subset.
> txbygene <- transcriptsBy(txdb, "gene")
> seqlevels(txbygene)
 [1] "chr2L"     "chr2R"     "chr3L"     "chr3R"     "chr4"      "chrX"     
 [7] "chrU"      "chrM"      "chr2LHet"  "chr2RHet"  "chr3LHet"  "chr3RHet" 
[13] "chrXHet"   "chrYHet"   "chrUextra"
> chr2L <- keepSeqlevels(txbygene, "chr2L")
> seqlevels(chr2L)
[1] "chr2L"
> 
> ## ---------------------------------------------------------------------
> ## renameSeqlevels 
> ## ---------------------------------------------------------------------
> 
> ## GAlignments:
> 
> seqlevels(gal)
[1] "seq1" "seq2"
> ## 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"))
Warning message:
In renameSeqlevels(gal, c(foo = "chr2")) : invalid seqlevels 'foo' ignored
> identical(seqlevels(gal), seqlevels(gal3))
[1] TRUE
> 
> ## TxDb:
> 
> seqlevels(txdb)
 [1] "chr2L"     "chr2R"     "chr3L"     "chr3R"     "chr4"      "chrX"     
 [7] "chrU"      "chrM"      "chr2LHet"  "chr2RHet"  "chr3LHet"  "chr3RHet" 
[13] "chrXHet"   "chrYHet"   "chrUextra"
> ## When the seqlevels of a TxDb are renamed, all future 
> ## extractions reflect the modified seqlevels.
> renameSeqlevels(txdb, sub("chr", "CH", seqlevels(txdb)))
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: dm3
# Organism: Drosophila melanogaster
# Taxonomy ID: 7227
# UCSC Table: ensGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Ensembl gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 29173
# exon_nrow: 76920
# cds_nrow: 62135
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-07 18:15:53 +0000 (Wed, 07 Oct 2015)
# GenomicFeatures version at creation time: 1.21.30
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> renameSeqlevels(txdb, c(CHM="M"))
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: dm3
# Organism: Drosophila melanogaster
# Taxonomy ID: 7227
# UCSC Table: ensGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Ensembl gene ID
# Full dataset: yes
# miRBase build ID: NA
# transcript_nrow: 29173
# exon_nrow: 76920
# cds_nrow: 62135
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-07 18:15:53 +0000 (Wed, 07 Oct 2015)
# GenomicFeatures version at creation time: 1.21.30
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> seqlevels(txdb)
 [1] "CH2L"     "CH2R"     "CH3L"     "CH3R"     "CH4"      "CHX"     
 [7] "CHU"      "M"        "CH2LHet"  "CH2RHet"  "CH3LHet"  "CH3RHet" 
[13] "CHXHet"   "CHYHet"   "CHUextra"
> 
> transcripts <- transcripts(txdb)
> identical(seqlevels(txdb), seqlevels(transcripts))
[1] TRUE
> 
> ## ---------------------------------------------------------------------
> ## restoreSeqlevels 
> ## ---------------------------------------------------------------------
> 
> ## Restore seqlevels in a TxDb to original values.
> ## Not run: 
> ##D txdb <- restoreSeqlevels(txdb)
> ##D 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
GRanges object with 5 ranges and 0 metadata columns:
                  seqnames    ranges strand
                     <Rle> <IRanges>  <Rle>
  [1]                 chr1    [1, 3]      *
  [2]                 chr2    [2, 4]      *
  [3]                 chr3    [3, 5]      *
  [4] chr1_gl000191_random    [4, 6]      *
  [5] chr1_gl000192_random    [5, 7]      *
  -------
  seqinfo: 5 sequences from an unspecified genome; no seqlengths
> grl <- split(gr,seqnames(gr))
> 
> ##GRanges
> keepStandardChromosomes(gr)
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    [1, 3]      *
  [2]     chr2    [2, 4]      *
  [3]     chr3    [3, 5]      *
  -------
  seqinfo: 3 sequences from an unspecified genome; no seqlengths
> 
> ##GRangesList
> keepStandardChromosomes(grl)
GRangesList object of length 3:
$chr1 
GRanges object with 1 range and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    [1, 3]      *

$chr2 
GRanges object with 1 range and 0 metadata columns:
      seqnames ranges strand
  [1]     chr2 [2, 4]      *

$chr3 
GRanges object with 1 range and 0 metadata columns:
      seqnames ranges strand
  [1]     chr3 [3, 5]      *

-------
seqinfo: 3 sequences from an unspecified genome; no seqlengths
> 
> plantgr <- GRanges(c(1:5,"MT","Pltd","wrong"), IRanges(1:8,width=5))
> keepStandardChromosomes(plantgr, species="Arabidopsis thaliana")
GRanges object with 7 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        1   [1,  5]      *
  [2]        2   [2,  6]      *
  [3]        3   [3,  7]      *
  [4]        4   [4,  8]      *
  [5]        5   [5,  9]      *
  [6]       MT   [6, 10]      *
  [7]     Pltd   [7, 11]      *
  -------
  seqinfo: 7 sequences from an unspecified genome; no seqlengths
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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