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

Celine Wuyts celinewuyts at hotmail.com
Sat Mar 8 18:54:33 CET 2014


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.
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?


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