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
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Michael
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