Assign sequence IDs to sequence names

Share:

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

1
2
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

1
2
3
4
5
6
7
8
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)