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Question: Cannot read plink files correctly
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gravatar for AR3513
5 months ago by
AR35130
AR35130 wrote:

Hello, 

I am trying to read PLINK files into R, using snpgdsBED2GDS(). However, it doesnt read it correctly. I have 1988 samples and 548476 SNPs, but the function reads it the other way around (i.e. 1988 samples and 548476 SNPs). See details below. Any help?

Thanks, 

Andrea

> mydata2 = snpgdsBED2GDS("lebanon_complete.bed", "lebanon_complete.bim", "lebanon_complete.fam", "HapMap2.gds")

Start snpgdsBED2GDS ...
    BED file: "lebanon_complete.bed" in the SNP-major mode (Sample X SNP)
    FAM file: "lebanon_complete.bim", DONE.
    BIM file: "lebanon_complete.fam", DONE.
Fri Jun  2 15:37:50 2017     store sample id, snp id, position, and chromosome.
    start writing: 548476 samples, 1988 SNPs ...
     Fri Jun  2 15:37:50 2017    0%
     Fri Jun  2 15:37:59 2017    100%
Fri Jun  2 15:38:03 2017     Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'HapMap2.gds' (262.1M)
    # of fragments: 39
    save to 'HapMap2.gds.tmp'
    rename 'HapMap2.gds.tmp' (262.1M, reduced: 252B)
    # of fragments: 18

 

ADD COMMENTlink modified 5 months ago by zhengx10 • written 5 months ago by AR35130
1
gravatar for zhengx
5 months ago by
zhengx10
United States
zhengx10 wrote:

Start snpgdsBED2GDS ...
    BED file: "lebanon_complete.bed" in the SNP-major mode (Sample X SNP)
    FAM file: "lebanon_complete.bim", DONE.
    BIM file: "lebanon_complete.fam", DONE.

You have used the wrong FAM and BIM files.

 

ADD COMMENTlink written 5 months ago by zhengx10
Ahh!! Thanks very much!! ________________________________ From: zhengx [bioc] <noreply@bioconductor.org> Sent: 02 June 2017 18:43:58 To: Rodriguez Martinez, Andrea Subject: [bioc] A: Cannot read plink files correctly Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User zhengx<https: support.bioconductor.org="" u="" 7950=""/> wrote Answer: Cannot read plink files correctly<https: support.bioconductor.org="" p="" 96608="" #96616="">: Start snpgdsBED2GDS ... BED file: "lebanon_complete.bed" in the SNP-major mode (Sample X SNP) FAM file: "lebanon_complete.bim", DONE. BIM file: "lebanon_complete.fam", DONE. You have used the wrong FAM and BIM files. ________________________________ Post tags: snprelate, Tutorial You may reply via email or visit A: Cannot read plink files correctly
ADD REPLYlink written 5 months ago by AR35130
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