I apologize in advance, I am new in the scripting business and am only using this for my project right now to graduate. I am not entirely sure how to format my text here correctly, I tried following the instructions on here but I don't think I am getting it right. To fix this, I hope I have written it down in such a way that it is easy to follow nevertheless and that I have given all the information necessary. I also couldn't tag the packages this topic concerns as they didn't come up on the list. Please let me know if I need to alter this in some way!
My issue: I am using the dartR package in R studio to work with DArTseq data. I have been using a tutorial for this and it has been working perfectly for me so far:
Now I want to convert the dartR objects into something I can use in SNPRelate. The tutorial mentions this step as well in chapter 17.4. I also googled outside of this tutorial and I found the same code for this (the name of my object is 'gl':
- gl2gds(gl, outfile = "gl2gds.gds", outpath = getwd())
- gds <- snpgdsOpen("g12gds.gds")
The part that is not working for me is the second line; loading in the new file in SNPRelate.
This is the message in my console:
gl2gds(gl, outfile = "gl2gds.gds", outpath = getwd())
Converting gl object to gds formatted file /Users/.../dartR-master/gl2gds.gds
gds <- snpgdsOpen("g12gds.gds")
Error in openfn.gds(filename, readonly, allow.duplicate = allow.duplicate, :
Can not open file 'g12gds.gds'. No such file or directory
I shortened the working directory for easier viewing with '/.../'
Can anyone help me to understand why the file is not found? In my understanding the file IS created, the name is correct. But why can't R find it?
I use the following packages following tutorials for both dartR and SNPRelate and they have all been installed and loaded correctly: