R: Transfer Nucleotide Codes / nids and SNPs / sids

code2snp {phyclust} | R Documentation

## 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)

### 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.

### 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.

### 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.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

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

### See Also

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

### Examples

    ## Not run:
    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)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]