phyclust (version 0.1-9)

nid.aid.cid: Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64)

Description

Transfer nids (0, 1, ..., 4) , aids (0, 1, ..., 21) and cids (0, 1, ..., 64).

Usage

### S3 methods for a list, vector or matrix (default).
nid2aid(nidseq, start = 1, end = NULL, drop.gap = FALSE, byrow = TRUE)
nid2cid(nidseq, start = 1, end = NULL, drop.gap = FALSE, byrow = TRUE)
cid2aid(cidseq)
aid2acode(aidseq, lower.case = FALSE)
acode2aid(acodeseq)

Arguments

nidseq

a numerical vector contains nucleotide ids, 0, 1, 2, 3, or 4.

cidseq

a numerical vector contains codon ids, 0, 1, ..., or 64.

aidseq

a numerical vector contains amino acid ids, 0, 1, ..., or 21.

acodeseq

a character vector contains amino acid codes.

start

the start site to translate.

end

the end site to translate.

drop.gap

ignore gaps if TRUE.

byrow

advanced option, default = TRUE.

lower.case

transfer in lower cases.

Value

• nid2aid and cid2aid returns a numerical vector containing amino acid ids, and nid2cid returns a numerical vector containing codon ids, aid2acode returns a character vector containing amino acid codes, and acode2aid returns a numerical vector containing amino acid ids.

Details

These functions are based on the internal object .nucleotide, .codon, .amino.acid, and .genetic.code to transfer sequences.

References

Phylogenetic Clustering Website: http://thirteen-01.stat.iastate.edu/snoweye/phyclust/

See Also

.nucleotide, .amino.acid, .codon, .genetic.code, code2nid.

Examples

### Test S3 methods by a vector
a.vector <- c("A", "C", "G", "-", "T", "A")
code2nid(a.vector)
nid2cid(code2nid(a.vector))
cid2aid(nid2cid(code2nid(a.vector)))
nid2aid(code2nid(a.vector))
aid2acode(nid2aid(code2nid(a.vector)))
acode2aid(aid2acode(nid2aid(code2nid(a.vector))))

### Test S3 methods by a matrix
a.matrix <- rbind(a.vector, a.vector, a.vector)
code2nid(a.matrix)
nid2cid(code2nid(a.matrix))
cid2aid(nid2cid(code2nid(a.matrix)))
nid2aid(code2nid(a.matrix))
aid2acode(nid2aid(code2nid(a.matrix)))
acode2aid(aid2acode(nid2aid(code2nid(a.matrix))))

### Test S3 methods by a list
a.list <- list(a.vector, a.vector)
code2nid(a.list)
nid2cid(code2nid(a.list))
cid2aid(nid2cid(code2nid(a.list)))
nid2aid(code2nid(a.list))
aid2acode(nid2aid(code2nid(a.list)))
acode2aid(aid2acode(nid2aid(code2nid(a.list))))