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GreenwoodLab / RVPedigree

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Reading genetic data from .bed files doesn't work #1

Open lckarssen opened 8 years ago

lckarssen commented 8 years ago

While trying to read genetic data from a Plink .bed file I got the following error message:

> askat.result <- ASKAT.region(y=pheno, X=covar, Phi=rel.mat,
type="bed",filename=geno.file, chr=4, startpos=0, endpos=170000, map=mymap)

Error in file(file, "rt") (from read.haplo.bedfile.R#27) : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'raw-GWA-data.bed.bim': No such file or directory

So probably the basename of the file should be used in read.haplo.bedfile.R instead of the full filename.

lckarssen commented 8 years ago

I will send a pull request with a fix later today.