export_genclone: export data file to Adegenet, Genetix and Arlequin

In dbailleul/RClone: Partially Clonal Populations Analysis

Description

These functions allow to transform a RClone table into files to work with Adegenet (R package), Genetix and Arlequin softwares.

Usage

export_genclone_genind(data1, ele)
export_genclone_genetix(data1, haploid = FALSE, ele, name)
export_genclone_arlequin(data1, haploid = FALSE, name)

Arguments

data1	a RClone table with only one population.
haploid	logical, option, if haploid = FALSE, data1 contains diploid data; if haploid = TRUE, haploid data.
ele	option, separator element for export.
name	option, name of the exported file.

Value

a genind object or a file for Genetix or Arlequin.

Note

For multi-population files, we recommend to use split function to cut the table into several tables, one for each population, and then combine lapply with the export functions.

Author(s)

Creator/Author: Diane Bailleul <[e-mail]>
Author: Sophie Arnaud-Haond <[e-mail]>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

Examples

data(posidonia)

#RClone to Adegenet:
res <- export_genclone_genind(posidonia, "/")
#library(adegenet)
#res2 <- df2genind(res, ploidy = 2, sep = "/")
#nAll(res2)

#RClone to Genetix:
export_genclone_genetix(posidonia, name = "test.txt")
#or
write.table(export_genclone_genetix(posidonia), "test2.txt", row.names = FALSE, 
sep = "\t", quote = FALSE)
#for genets only:
export_genclone_genetix(unique(posidonia), name = "test.txt")

#Rclone to Arlequin:
write.table(export_genclone_arlequin(posidonia), "file1.arp", row.names = FALSE,
 col.names = FALSE, quote = FALSE)
#or
export_genclone_arlequin(posidonia, haploid = FALSE, "file2.arp")
#for genets only:
export_genclone_arlequin(unique(posidonia), haploid = FALSE, "file2.arp")

#if several populations:
#res <- split(data, vecpop)
#lapply(res, function(x) export_genclone_genetix(x))
#lapply(res, function(x) export_genclone_arlequin(x))

dbailleul/RClone documentation built on May 17, 2021, 3:04 p.m.