writeGtypes: Write 'gtypes'

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Write gtypes

Description

Write a gtypes object to file(s).

Usage

writeGtypes(
  g,
  label = NULL,
  folder = NULL,
  by.strata = TRUE,
  as.frequency = FALSE,
  freq.type = c("freq", "prop"),
  as.haplotypes = TRUE,
  ...
)

Arguments

g	a gtypes object.
label	label for filename(s). Default is the gtypes description if present.
folder	folder where file(s) should be written to. If NULL, files are written to current working directory.
by.strata	if as.frequency == TRUE, calculate frequencies by strata?
as.frequency	logical indicating if haploid data should be output as frequency tables.
freq.type	if as.frequency == TRUE, write absolute frequencies ("freq") or proportions ("prop").
as.haplotypes	write sequences as haplotypes (TRUE) or individual sequences (FALSE).
...	optional arguments controlling what information is included in the genotype file and how it is formatted passed to as.matrix.

Details

Writes a comma-delimited (.csv) file of genotypes and if sequences are present, a .fasta file for each locus. If haploid and as.frequency is TRUE, then frequency tables for each locus are written to separate files.

Author(s)

Eric Archer [e-mail]

Examples

## Not run: 
# Write microsatellites with one column per locus
data(msats.g)
writeGtypes(msats.g, one.col = TRUE)

# Write control region data as frequency tables
data(dloop.g)
writeGtypes(dloop.g, as.frequency = TRUE)

## End(Not run)

EricArcher/strataG documentation built on June 8, 2025, 2:12 a.m.