Question：How Make The Raw Snp Or Plink Data Available For Numeric Regression,So What Is The Meaning Of Each Item In The Format?
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Entering edit mode
8.1 years ago

(1)In the SNP raw data from csv file. Allele1 - Forward, Allele2 - Forward, Allele1 - Top, Allele2 - Top,...

In the Illumina® SNP Genotyping “TOP/BOT” Strand and “A/B” Allele,there is no explanation for the Forward Allele.


(2) In the Plink data ,two forward allele columns from csv file（coupled with minor and major allele）can be used.

So

How make the raw SNP or Plink data available for numeric regression?If I want to make a regression ,which one column should I pick up with the Biallelic markers? Thanks!

snp plink allele • 4.4k views
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Entering edit mode
8.1 years ago
ff.cc.cc ★ 1.3k

Hi,

Plink data format (.ped/.map) or binary format (.bed/.bam) are regression ready, if you perform analysis with Plink (e.g. -model or -logistic or ... a lot of other options), and also if you import them in R.

In your case I suppose you still have to convert data from the Illumina sw (genomestudio) to a feasible report format.

So I suggest to look here, where you can find a Plink export plugin for genomestudio that allows you to create input files for PLINK