[adegenet-forum] read.PLINK alleles not properly read

[Celine Wuyts]

Hi,

I am new to this package but have been googling for a problem I encounter with the extract.PLINKmap function and cannot find an answer.

I read my SNP data from plink format with a standard line, choosing the appropriate files with .raw and .map extension from my directory as required.
x<-read.PLINK(file.choose(),map.file=file.choose(),parallel=F)
Worked perfectly, although it took more than an hour to finally get my genlight object built.
However, the SNP map information is not read as it should. The x$other$chromosome is a vector of NA's, as is x$other$position. I tried the extract.PLINKmap as well but it gave the same result.
Also, the x$alleles is empty (NULL) and the locNames are the original names with the letter of the allele that is counted added to it.
For example: SNP1909 becomes SNP1909_C. I assume that the fact that my SNP map information is not read properly is due to the fact that names of SNPs have changed and R cannot find any matches so to say. What did I do wrong and how can I fix it?

Also, I would like to subset my genlight object for individuals based on information (geographic grouping) in a seperate file. I thought about simply reading this information in x$other and working from their, but also this is not straightforward, as the seperate file contains more individuals and in a different order.

Last question: seems that not many functions that work for genind objects are implemented for genlight objects. Is there a workaround for this, other than converting genlight to data frame and data frame to a genind object?

Thanks.




 		 	   		  
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