Question: How to calculate r-squared with Haploview from different sources?
1
gravatar for analyticalavailable
3.4 years ago by
Ireland
analyticalavailable30 wrote:

I would like to get the r-squared for two SNPs in my population. One of the SNPs is in a mySQL db, and the other is currently also in a mySQL db, but I have the plink files for that one.

Can anyone advise me on how I will go about getting these into a format that Haploview will understand?

EDIT:

Just to clarify, I've two SNPs from different data sources on the patients. While they are indicated to be perfect proxies for each other (1000Genomes), they present different p-values when the Jonckheere-Tempstra test is performed, SNP-A (p=0.2192), SNP-B (p=0.0152). I've been asked to get the r-square between them.

Haploview accepts a plink format, I don't have the plink files for SNP-A, that is contained entirely within a mySQLdb, converted over from the SAS format of a previous student. I do have the plink files for SNP-B, but it is split into two separate plink datasets. Both datasets can be merged using plink, but there is still the issue of SNP-A not being available in a plink format.

haploview plink snps • 1.4k views
ADD COMMENTlink modified 3.4 years ago by zx87544.6k • written 3.4 years ago by analyticalavailable30

To clarify, do the samples overlap for these 2 SNPs?

ADD REPLYlink written 3.4 years ago by zx87544.6k

Yes, ~97% of them.

ADD REPLYlink written 3.4 years ago by analyticalavailable30

Someone mentioned to me that I could output each of the SNPs into an excel file, and do it from there. Then I would need a file with the pair of genotypes at each locus listed for each person. I'm actually a computer scientist, I've never used this tool before. Are we talking two columns, with each row a patient, and each column a SNP?

ADD REPLYlink written 3.4 years ago by analyticalavailable30
2
gravatar for zx8754
3.4 years ago by
zx87544.6k
London
zx87544.6k wrote:

If you have genotype for both SNPs for the same samples, simply create PED MAP files, (using Excel, text editor, command line...) then use plink for merging and calculating LD.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by zx87544.6k
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