Question: 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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gravatar for haoxiaokenuaa
7.6 years ago by
haoxiaokenuaa0 wrote:

(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!

allele plink snp • 4.3k views
ADD COMMENTlink modified 7.6 years ago by ff.cc.cc1.3k • written 7.6 years ago by haoxiaokenuaa0
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gravatar for ff.cc.cc
7.6 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

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

ADD COMMENTlink written 7.6 years ago by ff.cc.cc1.3k
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