PLINK CASE-CONTROL ANALYSIS

Question

[Nai]

I don't have vcf file. I rsid/snp id, chrom, position, growth parameters, case n control. Quality control, HWE, logistic regression.

[Pierre Lindenbaum]

question .

[Nai]

Dear Pierre,

Sorry, I would like to perform in Plink. The question is to generate .bed, .map. .fim files from csv files having Marker, variety and phenotype information. How will I separate case and control or should case and control in one file. I have phenotype and genotypic information for each marker. The information is like this:

PATIENT MARKER  ALLELE1 ALLELE2 CHROM   DIST    Sowing  Disease PLACE   XX  Seed    Pod Length  UREA
SWS1    RS55514 G   G   7   28028432    2016-04-17  LR  UP  1   79  1   9.3 6
SWS2    RS55514 A   G   7   28028432    2017-10-11  YR  MP  1   72  1   6.5 6
SWS3    RS55514 G   G   7   28028432            CH  1   65  1   12  6

[brunobsouzaa]

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[Nai]

Thank you. I prepared .ped and .map file, Now I would like to calculate Odds ratio, MAF, pvalue for each marker. When I executed the command plink --file Wei --assoc --maf 0.05 --out run1 I got NA in Odds ratio column.

Simultaneously I have to predict Odds ratio and pvalue for each environmental factor or clinical factors for particular SNP.