[adegenet-forum] Error when converting STRUCTURE file to genind

[Spencer Bruce]

Thanks, but still getting the same error message below:

Converting data from a STRUCTURE .stru file to a genind object...

Error in mat[, (ncol(mat) - p + 1):ncol(mat)] :
  only 0's may be mixed with negative subscripts
> traceback()
2: read.structure(file, missing = missing, quiet = quiet, ...)
1: import2genind("Bird.str", missing = "missing", onerowperind = 1,
       n.ind = 239, n.loc = 98, col.lab = 1, col.pop = 2, ask = FALSE)
>

On Wed, Dec 17, 2014 at 5:08 PM, Vikram Chhatre <crypticlineage at gmail.com>
wrote:
>
> I use this:
>
> Bird_genind <- import2genind('Bird.str', missing='missing',
> onerowperind=1, n.ind=10, n.loc=20, col.lab=1, col.pop=2, ask=FALSE)
>
> This assumes you have data coded as one row per individual, with 10
> individuals, 20 loci, individual labels in column 1, population labels in
> column 2.  Also, I code missing data with a '-9'.
>
> V
>
> On Wed, Dec 17, 2014 at 4:09 PM, Spencer Bruce <goatsrunfaster at gmail.com>
> wrote:
>
>> I get the following Error Message when I attempt to convert a STRUCTURE
>> file to a genind object:
>>
>> Converting data from a STRUCTURE .stru file to a genind object...
>>
>> Error in mat[, (ncol(mat) - p + 1):ncol(mat)] :
>>   only 0's may be mixed with negative subscripts
>> > traceback()
>> 2: read.structure(file, missing = missing, quiet = quiet, ...)
>> 1: import2genind("Bird.str")
>>
>> I've looked through the data and everything is in order, this runs fine
>> in STRUCTURE and I've never had problems importing STRUCTURE files before.
>>
>> Just for the record this is SNP data in haploid format where G,C,A,T is
>> coded for as 1,2,3,4 respectively.
>>
>> Any help would be greatly appreciated!
>>
>> -Spencer
>>
>> --
>> Spencer A Bruce
>> 113 Hill St.
>> Troy, NY 12180
>> 518 225 0787
>>
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
>>
>

-- 
Spencer A Bruce
113 Hill St.
Troy, NY 12180
518 225 0787
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