[R] convert.snp.ped in GenAbel

aoife doherty aoife.m.doherty at gmail.com
Tue Dec 1 14:51:39 CET 2015

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?


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