code2nid: Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)

In phyclust: Phylogenetic Clustering (Phyloclustering)

Transfer Codes (A, G, C, T, -) and nids (0, 1, 2, 3, 4)

Description

Transfer nucleotide codes (A, G, C, T, -) and nucleotide ids (0, 1, 2, 3, 4).

Usage

### S3 methods for a list, vector or matrix (default).
code2nid(codeseq)
nid2code(nidseq, lower.case = TRUE)

Arguments

codeseq	a character vector contains nucleotide codes, A, G, C, T, or -.
nidseq	a numerical vector contains nucleotide ids, 0, 1, 2, 3, or 4.
lower.case	transfer in lower cases.

Details

These functions are based on the internal object .nucleotide to transfer codes and nids.

Value

code2nid returns a numerical vector containing nucleotide ids, and nid2code returns a character vector containing nucleotide codes.

Author(s)

Wei-Chen Chen [e-mail]

References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

See Also

.nucleotide, snp2sid, sid2snp, code2snp, snp2code.

Examples

## Not run: 
library(phyclust, quiet = TRUE)

a <- c("A", "C", "G", "-", "T")
code2nid(a)
nid2code(code2nid(a)) 

## End(Not run)

phyclust documentation built on Sept. 8, 2023, 6 p.m.