gl2fasta: Concatenates DArT trimmed sequences and outputs a FASTA file

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Concatenates DArT trimmed sequences and outputs a FASTA file

Description

Concatenated sequence tags are useful for phylogenetic methods where information on base frequencies and transition and transversion ratios are required (for example, Maximum Likelihood methods). Where relevant, heterozygous loci are resolved before concatenation by either assigning ambiguity codes or by random allele assignment.

Usage

gl2fasta(
  x,
  method = 1,
  outfile = "output.fasta",
  outpath = tempdir(),
  probar = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
method	One of 1 | 2 | 3 | 4. Type method=0 for a list of options [method=1].
outfile	Name of the output file (fasta format) ["output.fasta"].
outpath	Path where to save the output file (set to tempdir by default)
probar	If TRUE, a progress bar will be displayed for long loops [default = TRUE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

Four methods are employed:

Method 1 – heterozygous positions are replaced by the standard ambiguity codes. The resultant sequence fragments are concatenated across loci to generate a single combined sequence to be used in subsequent ML phylogenetic analyses.

Method 2 – the heterozygous state is resolved by randomly assigning one or the other SNP variant to the individual. The resultant sequence fragments are concatenated across loci to generate a single composite haplotype to be used in subsequent ML phylogenetic analyses.

Method 3 – heterozygous positions are replaced by the standard ambiguity codes. The resultant SNP bases are concatenated across loci to generate a single combined sequence to be used in subsequent MP phylogenetic analyses.

Method 4 – the heterozygous state is resolved by randomly assigning one or the other SNP variant to the individual. The resultant SNP bases are concatenated across loci to generate a single composite haplotype to be used in subsequent MP phylogenetic analyses.

Trimmed sequences for which the SNP has been trimmed out, rarely, by adapter mis-identity are deleted.

The script writes out the composite haplotypes for each individual as a fastA file. Requires 'TrimmedSequence' to be among the locus metrics (@other$loc.metrics) and information of the type of alleles (slot loc.all e.g. 'G/A') and the position of the SNP in slot position of the “'genlight“' object (see testset.gl@position and [e-mail] for how to format these slots.)

Value

A new gl object with all loci rendered homozygous.

Author(s)

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

Examples

 
gl <- gl.filter.reproducibility(testset.gl,t=1)
gl <- gl.filter.overshoot(gl,verbose=3)
gl <- gl.filter.callrate(testset.gl,t=.98)
gl <- gl.filter.monomorphs(gl)
gl2fasta(gl, method=1, outfile='test.fasta',verbose=3)

test <- gl.subsample.loci(platypus.gl,n=100)
gl2fasta(test)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.