rankSeqlevels {GenomeInfoDb} | R Documentation

## 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

`seqnames` | A character vector or factor containing sequence names.
`X.is.sexchrom` | A logical indicating whether X refers to the sexual chromosome or to chromosome with Roman Numeral X. If `NA`, `rankSeqlevels` does its best to "guess".

### 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. Pagès 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)

[Package GenomeInfoDb version 1.16.0 Index]