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zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)
https://hibag.s3.amazonaws.com/index.html
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Invalid prefix in the PLINK BED file error message #3

Closed MarthaDuke closed 6 years ago

MarthaDuke commented 6 years ago

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

zhengxwen commented 6 years ago

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.

MarthaDuke commented 6 years ago

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.

MarthaDuke commented 6 years ago

It may have been a Windows issue, it is working now.