minor allele frequency from genotype data

Question

[iphoenix2100]

Hi all,

Sorry for this elementary question, I am new to pop. genetics and I got to calculare maf from a datasets - that has data on the snp genotypes.

Example dataset:

MarkerName  Chr     A1    A2    N-total    POSITION    beta        SE       P.value
rs123       3       G     A     15000      450040      0.0598      0.01172  0.44564
rs124       3       C     T     10456      454544      0.063376    0.01107  0.11444
rs125       3       A     T     5254       447846      0.097821    0.12456  0.00144
rs126       3       G     A     16000      477946      0.000322    0.01245  0.04456
rs127       3       C     A     6464       444789      0.0001476   0.0444   0.14465

How can I do it in R.. I came to know of a package called hardyweinberg with functions like MAF and MAC

Any suggestions will be of great help

Thanks
Chris

[Sean Davis]

Do you want to look up the SNPs in dbSNP or 1000genomes to get the MAF, or do you want to calculate it from your own data? If the latter, you'll need the actual genotypes. The file you are showing is not enough.