Hi,
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.
Code:
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:
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.
Sincerely,
PD
PhD Candidate
University of Texas at Houston
School of Public Health
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