[Bioc-devel] Help with GWASTools

[Qian Liu]

Hi,

Try the following. Just print "bed.fn" to see if they are imported
correctly.  And use "snpgdsBED2GDS(... verbose=TRUE)" to print more
detailed information or error log.

Qian Liu
Bioconductor Core Team
Roswell Park Cancer Institute

library(SNPRelate)
(bed.fn <- system.file("extdata", "plinkhapmap.bed.gz",
package="SNPRelate"))

 [1]
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.bed.gz"

(fam.fn <- system.file("extdata", "plinkhapmap.fam.gz",
package="SNPRelate"))

 [1]
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.fam.gz"

(bim.fn <- system.file("extdata", "plinkhapmap.bim.gz",
package="SNPRelate"))

 [1]
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.bim.gz"

gdsfile <- "snps.gds"



snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, gdsfile, cvt.chr="int",
cvt.snpid="int", verbose=TRUE)


 Start snpgdsBED2GDS ...
         BED file:
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.bed.gz"
in the SNP-major mode (Sample X SNP)
         FAM file:
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.fam.gz",
DONE.
         BIM file:
"/home/qian/R/x86_64-pc-linux-gnu-library/3.5-bioc-3.7/SNPRelate/extdata/plinkhapmap.bim.gz",
DONE.
 Mon Feb 12 14:37:07 2018        store sample id, snp id, position, and
chromosome.
         start writing: 60 samples, 5000 SNPs ...
         Mon Feb 12 14:37:07 2018        0%


         Mon Feb 12 14:37:07 2018        100%
 Mon Feb 12 14:37:07 2018        Done.
 Optimize the access efficiency ...
 Clean up the fragments of GDS file:
     open the file 'snps.gds' (100.6K)
     # of fragments: 42


     save to 'snps.gds.tmp'
     rename 'snps.gds.tmp' (100.3K, reduced: 264B)
     # of fragments: 20



f <- openfn.gds(gdsfile)
f

 File: /home/qian/snps.gds (100.3K)
 +    [  ] *
 |--+ sample.id   { Str8 60 LZMA_ra(53.8%), 265B }


 |--+ snp.id   { Int32 5000 LZMA_ra(11.7%), 2.3K }
 |--+ snp.rs.id   { Int32 5000 LZMA_ra(20.8%), 4.1K }


 |--+ snp.position   { Int32 5000 LZMA_ra(78.5%), 15.3K }
 |--+ snp.chromosome   { UInt8 5000 LZMA_ra(3.00%), 157B } *


 |--+ snp.allele   { Str8 5000 LZMA_ra(13.8%), 2.7K }
 |--+ genotype   { Bit2 60x5000, 73.2K } *
 \--+ sample.annot   [ data.frame ] *
    |--+ sex   { Str8 60 LZMA_ra(136.7%), 89B }


    \--+ phenotype   { Int32 60 LZMA_ra(37.5%), 97B }


closefn.gds(f)

On Thu, Feb 8, 2018 at 12:19 PM, Dharia, Priyadarshani P <
Dharia.Priyadarshani at uth.tmc.edu> wrote:

> 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
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]