Assign sequence IDs to sequence names

Description

rankSeqlevels assigns a unique ID to each unique sequence name in the input vector. The returned IDs span 1:N where N is the number of unique sequence names in the input vector.

orderSeqlevels is similar to rankSeqlevels except that the returned vector contains the order instead of the rank.

Usage

rankSeqlevels(seqnames, X.is.sexchrom=NA)
orderSeqlevels(seqnames, X.is.sexchrom=NA)

Arguments

Value

An integer vector of the same length as seqnames that tries to reflect the “natural” order of seqnames, e.g.,chr1, chr2, chr3, ...

The values in the returned vector span 1:N where N is the number of unique sequence names in the input vector.

Author(s)

H. Pages for rankSeqlevels, orderSeqlevels added by Sonali Arora

See Also

• sortSeqlevels for sorting the sequence levels of an object in "natural" order.

Examples

library(BSgenome.Scerevisiae.UCSC.sacCer2)
rankSeqlevels(seqnames(Scerevisiae))
rankSeqlevels(seqnames(Scerevisiae)[c(1:5,5:1)])

newchr <- paste0("chr",c(1:3,6:15,4:5,16:22))
newchr
orderSeqlevels(newchr)
rankSeqlevels(newchr)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/rankSeqlevels.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rankSeqlevels
> ### Title: Assign sequence IDs to sequence names
> ### Aliases: rankSeqlevels orderSeqlevels
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(BSgenome.Scerevisiae.UCSC.sacCer2)
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> rankSeqlevels(seqnames(Scerevisiae))
 [1]  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18
> rankSeqlevels(seqnames(Scerevisiae)[c(1:5,5:1)])
 [1] 1 2 3 4 5 5 4 3 2 1
> 
> newchr <- paste0("chr",c(1:3,6:15,4:5,16:22))
> newchr
 [1] "chr1"  "chr2"  "chr3"  "chr6"  "chr7"  "chr8"  "chr9"  "chr10" "chr11"
[10] "chr12" "chr13" "chr14" "chr15" "chr4"  "chr5"  "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22"
> orderSeqlevels(newchr)
 [1]  1  2  3 14 15  4  5  6  7  8  9 10 11 12 13 16 17 18 19 20 21 22
> rankSeqlevels(newchr)
 [1]  1  2  3  6  7  8  9 10 11 12 13 14 15  4  5 16 17 18 19 20 21 22
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>