Converting to genepop

[Vanessa Morris]

Hi dartR team,

Can I please get your help converting a dartR file to genepop file?

I converted my data file to genlight:

gen <- new("genlight", glhw.filt)
gpop <- gl2genepop(gen, outfile ="glhw.filt.gen")

but then I receive the following error when using gl2genepop:

 stop("Fatal Error: Detected Presence/Absence (SilicoDArT) data. Please provide a SNP dataset\n")

Any advice?

Many thanks,

Vanessa

[Jose Luis Mijangos]

Hi Vanessa,

Based on the information you provided, it appears that you're using the gl2genepop function code that was posted in this forum four years ago. This function is now implemented in dartR. To resolve the issue, please follow these steps:

1. Ensure you have the latest version of dartR.base installed on your computer. You can install it using the following code:

   install.packages("dartR.base")

   If you encounter any issues during installation, please refer to our tutorial "Tutorial_2_dartR_Installation_2-Aug-24.pdf," available for download at: http://georges.biomatix.org/dartR.

2. Remove the function you sourced ("gl2genepop.R") by either:

   • Clearing your workspace, or
   • Removing the function directly from your environment.
     If you need guidance, refer to "Tutorial 1: RStudio Refresher."

3. Read your data using one of dartR's reading functions:

   • gl.read.csv
   • gl.read.dart
   • gl.read.fasta
   • gl.read.PLINK
   • gl.read.silicodart
   • gl.read.vcf

   For more details, see:

   • Tutorial 3A: Data Input and Data Structures (DArT)
   • Tutorial 3B: Data Input and Data Structures (non-DArT)

4. Convert your genlight object using the following approach:

library(dartRverse)

 t1 <- gl.read.dart("your_DArT_report") 

gl2genepop(t1, outpath = getwd())

Let me know if this resolves the issue or if you need further assistance.

Best,
Luis

[Vanessa Morris]

Got the genepop file! Thank you very much.

All the best,

Vanessa