[R] convert.snp.ped in GenAbel

Michael Dewey lists at dewey.myzen.co.uk
Tue Dec 1 15:34:57 CET 2015


Dear Aoife

I do not know the insides of GenABEL but it may be looking for the map 
file first so in fact may not be able to find the ped file either.

1 - Are you sure the files are named as you state?
2 - Are you sure they are placed in ~ which seems an unlikely place to 
put them.

On 01/12/2015 13:51, aoife doherty wrote:
> Having a problem with convert.snp.ped in GenABEL (on linux).
>
> My map file looks like this (tab-separated) (called Genotype.map)
>
>
> chrom name position
>
> 13   SNP1   39703523
>
>
> My ped file looks like this (Called Genotype.ped)
>
> PF1 PF1 0 0 2 -9 C C
>
> PF2 PF2 0 0 2 -9 C A
>
> PF3 PF3 0 0 1 -9 C C
>
> PF4 PF4 0 0 1 -9 C C
>
>
> The commands I'm using are:
>
>> library("GenABEL")
>
>> data <-convert.snp.ped(pedfile="~/Genotype.ped"
> ,mapfile="~/Genotype.map", outfile="~/Genotype.out")
>
>
> The error I get is:
>
> Error in convert.snp.ped(pedfile = "~/Genotype.ped", : could not open file
> '~/Genotype.map' !
>
>
> Any idea? It's in the same directory as the ped file, so I don't know why
> it can find the ped file and not the map file?
>
>
> Thanks
>
> 	[[alternative HTML version deleted]]
>
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-- 
Michael
http://www.dewey.myzen.co.uk/home.html



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