Question

Cannot read plink files correctly

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AR3513 • 0

@ar3513-11025

Last seen 4.2 years ago

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

snprelate Tutorial • 1.9k views

ADD COMMENT • link updated 7.5 years ago by zhengx ▴ 30 • written 7.5 years ago by AR3513 • 0

score 1 · Answer 1 · 2017-06-02

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zhengx ▴ 30

@zhengx-7950

Last seen 5.3 years ago

United States

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 COMMENT • link 7.5 years ago zhengx ▴ 30

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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 REPLY • link 7.5 years ago AR3513 • 0