Cannot read plink files correctly
1
0
Entering edit mode
AR3513 • 0
@ar3513-11025
Last seen 14 months 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 • 819 views
ADD COMMENT
1
Entering edit mode
zhengx ▴ 30
@zhengx-7950
Last seen 2.2 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
0
Entering edit mode
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

Login before adding your answer.

Traffic: 190 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6