How to calculate LD values of SNP based on chromosomal positions and their call rate?

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7.1 years ago

blacktomato27 ▴ 70

Hi to all Good Afternoon

I have file containing SNPs (affy 44k chip) with their call rate and chromosomal positions with me and these belongs to rice crop. Now how can i calculate LD values (r2) for these SNPs, my basic objective is to select tag SNPs based on LD for genotyping work. any help with any R packages or own functions in this regard will be highly appreciated Thanks in Advance

regards

SNP snp R • 2.2k views

ADD COMMENT • link 7.1 years ago by blacktomato27 ▴ 70

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To calculate LD you need a set comprising many genotypes (similar hapmap or 1kG, see also 1000 Genomes Ld Calculation ) from possibly many populations, do you have that? A quick google search did not reveal a genome wide public resource like that, but some older papers studying a selection of genotypes.

ADD REPLY • link 7.1 years ago by Michael 55k

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You can try to convert the data to PLINK format and then run a LD analysis there. Affymetrix PowerTools has a function that converts genotype data to PLINK format: https://www.affymetrix.com/support/developer/powertools/changelog/apt-format-result.html

ADD REPLY • link 7.1 years ago by Kevin Blighe 88k

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