Invalid prefix in the PLINK BED file error message
Closed this issue · 3 comments
The hlaBED2Geno function fails when I try to read in the BED file. If I use it as written, I get the error message: Error in hlaBED2Geno(fam.fn = ".fam", bim.fn = ".bim", bed.fn = ".bed") :
Cannot open the file .bed.
If I name the bed.fn separately, I get the message in the subject line. PLINK has no issues with the BED file. I made a PED and MAP file and then remade the BED file.
Thank you for any assistance.
Martha Butterworth
martha.butterworth@epi.usf.edu
You should use
hlaBED2Geno(fam.fn = "your_geno_file.fam", bim.fn = "your_geno_file.bim", bed.fn = "your_geno_file.bed")
your_geno_file should be replaced by your own PLINK file.
I'm sorry I wasn't very clear. I did use my PLINK file names as you indicated above and got the error message
Error in hlaBED2Geno(fam.fn = ".fam", bim.fn = ".bim", bed.fn = ".bed") :
Cannot open the file .bed.
The function seemed OK with the .fam and .bim files.
It may have been a Windows issue, it is working now.