[Bioc-devel] Help with GWASTools

Dharia, Priyadarshani P Dharia.Priyadarshani at uth.tmc.edu
Thu Feb 8 18:19:48 CET 2018


  I am a graduate student at University of Texas School of Public health, and I am using GWASTools for the first time. I am trying to upload PLINK files to use, but I am getting an error which I cannot understand. I would appreciate if you could help me with the same.


bed.fn <- system.file("C:/Users/PLINK/tissue_all1", "plinkhapmap.bed.gz", package = "SNPRelate")
fam.fn <- system.file("C:/Users/PLINK/tissue_all1", "plinkhapmap.fam.gz", package = "SNPRelate")
bim.fn <- system.file("C:/Users/PLINK/tissue_all1", "plinkhapmap.bim.gz", package = "SNPRelate")
gdsfile <-"snps.gds"
snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, gdsfile, cvt.chr="int", cvt.snpid="int", verbose=FALSE)


Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  :
  can only read from a binary connection
In addition: Warning message:
In file(filename, "rb") :
  file("") only supports open = "w+" and open = "w+b": using the former

Thank you for all your help.

PhD Candidate
University of Texas at Houston
School of Public Health

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