I'm currently trying to import a microsatellite dataset into the R package adegenet. I 'should' be able import structure, genepop or FSTAT files, but I'm having a heck of a time! (I am attempting to import a STRUCTURE file).
This is my recurring error:
Error in if (!toupper(.readExt(file)) %in% c("STR", "STRU")) stop("File extension .stru expected") :
argument is of length zero
Maybe I'm using the wrong input file? (The project data file generated by structure? the tab delimited file I originally import into STRUCTURE?) I've tried manually forcing the file into the .stu or .stru extension but still get the same error. What would be really great was if there was some sort of sample data file available lol.
I have been able to read in the data using the df2genind function, but have issues if I include ANY extra data (such as population, which is the reason I wanted to use adegenet to begin with).
Any help of troubleshooting tips would be greatly appreciated. Thanks!
I am using the genepop format and replace the extension as ".gen". Have you tried that? The sample file could be:
--------------------------------------------------
SSR data of rust from Pakistan [Title line]
RJN3 [Locus 1]
RJO18 [Locus 2]
RJN13 [Locus 3]
Pop
PK13_14 , 228228 319319 150153 339339
PK14_14 , 228228 319319 150153 339339
PK15_14 , 225228 316319 150150 339343
So silly, I was including extra arguments. Thanks!
I literally only needed:
obj
I am facing the same problem using of importing data in Fstat format. Kindly hrelp!
I have only imported structure files into adegenet. If you are using a file that already works in structure you first need to manually save the input file with the extension .stru . (It is likely a .txt or .csv file at the moment). Then it's as simple as:
obj
Hi everyone,
If you ONLY want to have a certain idea of the distribution of your data under the DAPC analysis, you can do:
-Open r
-write: library(adegenet)
-write: adegenetServer("DAPC"), and add your file from GENEPOP, FSTAT or STRUCTURE
It will open a windowslike the one attached in this message.
Regarding the problems about the how to open the files (and no matter if your file is .gen, .dat or .stru), you have to copy your file to the main folder of the adegenet package since the system.file search as the main folder (/) the adegenet folder.
C:\Program Files\R\R-3.2.2\library\adegenet\files
obj
Hi,
I obtain the scatterplot for my microsatellite data containing 4 populations.Is there any options that we can make the colour of each geographical region specific?
Hi Manal,
In the web adegenetServer, you have several options to change the colour of your data. The options are in the left side of the menu.
Hope that can help
Best
Ariel
Hello
Try importing a Genepop file....it is the easiest way.
good luck
I am using adegenet for the first time. I have a large data set exported from Stacks2 'populations' script as structure file.
In Win10 and Rstudio I ran:
D
I am new on adegenet. I exported a vcf file with 225045 loci to structure file in PGDspider.
In Win10 and Rstudio I ran
obj
Please I need help.. Attached is a subset of snps data in HapMap format. How do I convert it to genepop or FSTAT format? I need it to be convert to be able to estimate effective population size.
Hello Moshood
I have no experience with HapMap files, but inspecting yours I think you may manually extract the genotype relevant information in a separate excel file; first row: loci, first column: samples Id and may be a second column with population information. It will be suitable to be imported in GenAlEx:https://biology-assets.anu.edu.au/GenAlEx/Download.html, from wich you can export your data in multiple formats. For further conversion e.g., to Arlequin you can visit: https://genepop.curtin.edu.au/genepop_op7.html. Notice that you may inspect the output files in order to make corrections before they can be successfully used in other applications.
Good luck
Roberto
I am also 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 also import the data using the df2genind function but then I have problem when I include the population data later on (the same way as in the question).
the error that I get while adding population label is follow:
pop(obj)
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