phyclust (version 0.1-34)

code2snp: Transfer Nucleotide Codes / nids and SNPs / sids

Description

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

Usage

### S3 methods for a list, vector or matrix (default).
code2snp(codeseq)
snp2code(snpseq, half = TRUE)
nid2sid(nidseq)
sid2nid(sidseq, half = TRUE)

Value

code2nid returns a character vector containing nucleotide ids, and

nid2code returns a character vector containing nucleotide codes.

nid2sid returns a numerical vector containing SNP ids, and

sid2nid returns a numerical vector containing nucleotide ids.

Arguments

codeseq

a character vector contains nucleotide codes, A, G, C, T, or -.

snpseq

a character vector contains SNPs, 1, 2, or -.

half

nucleotide codes will be half assigned, see the ‘Details’ for more information.

nidseq

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

sidseq

a numerical vector contains SNP ids, 0, 1, or 2.

Author

Wei-Chen Chen

Details

These functions are based on the internal object .nucleotide and .snp to transfer nucleotide codes and SNPs. For code2snp, A, G are transfered to 1, and C, T are transfered to 2. For snp2code, 1 is transfered half to A and G, and 2 is transfered half to C and T if half = TRUE. Otherwise, 1 is all transfered to A, and 2 is all transfered to C.

References

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

See Also

.nucleotide, .snp, code2nid, nid2code, snp2sid, sid2snp.

Examples

if (FALSE) {
library(phyclust, quiet = TRUE)

# For codes
a.vector <- c("A", "C", "G", "-", "T")
code2snp(a.vector)
snp2code(code2snp(a.vector))
snp2code(code2snp(a.vector), half = FALSE)

# For ids
a.sid.vector <- c(0, 2, 1, 4, 3)
nid2sid(a.sid.vector)
sid2nid(nid2sid(a.sid.vector))
sid2nid(nid2sid(a.sid.vector), half = FALSE)

# Test list
a.list <- list(a, a)
code2snp(a.list)
snp2code(code2snp(a.list))
snp2code(code2snp(a.list), half = FALSE)

# Test matrix
a.matrix <- rbind(a, a)
code2snp(a.matrix)
snp2code(code2snp(a.matrix))
snp2code(code2snp(a.matrix), half = FALSE)
}