There are two R functions to convert from PLINK to GenABEL files: convert.snp.ped() (which inputs PLINK's *.ped and *.map files) and convert.snp.tped() (same for *.tped and *.tfam). An error happened when I tried to use convert.snp.ped() and R was forced to close. I had no problems with convert.snp.tped(). I know of one person who experienced the same issue although I do not know whether the same error message was prompt (and the cause of the problem).
On the other hand, be aware that any of the two functions (although both use as input files containing the phenotypic information) will only produce one of the input files (*.raw) for the GenABEL function that loads data: load.gwaa.data(). The second input file (*.dat) will have to be produced for instance from the *.tfam file. This means that (1) *.tfam does not have header and and *.dat must have (at least 'id' and 'sex' fields are required) and (2) PLINK uses 1/2 coding for sex by default whereas load.gwaa.data() uses 1/0. On the other hand, one would have to create anyway the *.dat file anyway if using a alternative phenotype file in PLINK (to allow for >1 phenotype or covariates). It is not the end of the world but it makes the conversion a bit less direct than expected...
Maybe somebody can add his/her experience?
