rankSeqlevels: Assign sequence IDs to sequence names

Description Usage Arguments Value Author(s) See Also Examples

View source: R/rankSeqlevels.R

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

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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. Pag<c3><a8>s for rankSeqlevels, orderSeqlevels added by Sonali Arora

See Also

Examples

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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)

GenomeInfoDb documentation built on Oct. 6, 2017, 2:03 a.m.