Question: How I can convert genotype data in a variety of pedigree formats R
0
gravatar for BlackHole
20 months ago by
BlackHole0
RF
BlackHole0 wrote:

I have a genotype data as a matrix of 10 samples (columns) and 560 000 SNPs (raws). I want to convert this data for further analysis , but have not MAP and PED file (PLINK format) to use GenABEL and I don't know any ways to do this conversion.

Here's a few rows and columns to show you what it looks like:

            S1  S2  S3  S4  S5
rs75406208  CC  CC  CG  CG  NA
rs200142685 AG  AG  GG  GG  GG
rs369829527 NA  NA  GG  GG  GG
rs76412254  GG  GG  GG  GG  GG
rs80033621  AA  AA  AA  AA  AA
rs62608737  GG  GG  GG  GG  GG
rs373506129 NA  NA  CC  CC  CC

Does anyone know any way to do it?

Thanks in advance.

snp R • 726 views
ADD COMMENTlink modified 17 months ago by guardianpatch0 • written 20 months ago by BlackHole0

Perhaps I missed something, but what's the D?

ADD REPLYlink written 20 months ago by WouterDeCoster30k

D is deletion I is inversion And I have many polymorphisms such as AG, AT, AA , GG, CC, CG, TT

ADD REPLYlink written 20 months ago by BlackHole0
1

I is insertion and not inversion that is something else

ADD REPLYlink written 20 months ago by Floris Brenk830

of course, i confused

ADD REPLYlink written 20 months ago by BlackHole0

This is weird. So you have a deletion for snp rs144430729, while that's a C/T SNP. Doesn't make sense to me. How did you obtain this data?

ADD REPLYlink written 20 months ago by WouterDeCoster30k

It is not my data, I got them from my colleagues, to conduct a joint analysis with the metabolome

ADD REPLYlink modified 20 months ago • written 20 months ago by BlackHole0

If this is sequencing data, try to get the original output. That will make things less painful and less error-prone.

ADD REPLYlink written 20 months ago by WouterDeCoster30k
0
gravatar for Floris Brenk
20 months ago by
Floris Brenk830
USA
Floris Brenk830 wrote:

Creating the ped file is easy with the information you already have. see for the format here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml just transpose what you have now and add a few columns:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female; other=unknown)
 Phenotype

For the map file you have to be a bit more creative and get the actual chromosome location etc of the snps probably by extracting it from dbsnp or similar.

 CHR RS-number score BP
 1  rs123456  0  1234555
ADD COMMENTlink written 20 months ago by Floris Brenk830

I try to upload my data in dbsnp, but the end result was a blank sheet, and I got message that RS number(s) not found in dbSNP

ADD REPLYlink written 20 months ago by BlackHole0
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