I am trying to import a structure input file into the R package adegenet. I am going round and round and still not able to figure it out yet
This is the error I am getting:
Error in mat[, (ncol(mat) - p + 1):ncol(mat)] :
only 0's may be mixed with negative subscripts
I have 363 genotypes with 1000 markers and 2nd column is pop.label.
I can import the data using the df2genind function but then I have problem when I include the population data later on (which is the reason I wanted to use adegenet in the first place).
the error that I get while adding population label is follow:
pop(obj)
I'm far from being an R expert, but whenever I use adegenet I create a genind file just with my genetic data, and then add all the extra info to it.
In your particular case, once you have your genind you could create a csv file in Excel (in which the order of the samples matches the order in your genind file) and specify the population there. The first cell of the column has the title (let's say you named the column "population"), so when you load this csv to R you set header= TRUE.
Then you load this csv file to R and use:
popNames(your_genind)
Dear @Alberto Fameli thank you for sharing your knowledge. I tried the way you mentioned as well and i get the followinh error.
"Vector length does not match number of populations"
I understand it is because of something to do with my input files but I couldn't figure it out yet.
Did you ever face this kind of error?
Thanks again for your support and time
If your csv file containing the population names has 363 lines and your genind file also has 363 lines, there shouldn't be a "vector length" error.
Have you tried converting it from Structure to genepop format in PGDSpider?
http://www.cmpg.unibe.ch/software/PGDSpider/
- Badges
- Science topic
- Similar topics
- Philosophy
- Philosophy Of Science
- Reasoning