How to calculate LD values of SNP based on chromosomal positions and their call rate?
0
0
Entering edit mode
6.6 years ago

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 • 2.1k views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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

Login before adding your answer.

Traffic: 2361 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6