scan the SNP variation sites from a given multiple sequence alignment

snp_scan {snp_toolkit}

R Documentation

scan the SNP variation sites from a given multiple sequence alignment

Description

fasta sequence data

Usage

snp_scan(nt, ref.index,
    pureMode = FALSE,
    monomorphic = FALSE,
    vcf.output.filename = NULL);

Arguments

a FastaFile multiple sequence alignment nucleotide sequence collection for scan the SNP variation sites. [as FastaFile]

ref.index

the index number of the reference sequence in the input multiple sequence alignment collection, which is used as the reference for make the SNP calling. [as string]

pureMode

only accept the pure SNP variations? if this parameter is TRUE, then the SNP sites that contains mixed variation information will be ignored. [as boolean]

monomorphic

include the monomorphic sites in the SNP scanning result?. [as boolean]

vcf.output.filename

a by-ref parameter for get the file path of the generated VCF format SNP variations output file. [as String&]

Authors

seqtoolkit

Value

a SNPsAln SNP variations analysis result object.

clr value class

SNPsAln

[Package snp_toolkit version 1.0.0.0 Index]