Question

MAF in R

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2.5 years ago

gosssheen • 0

Hello,

I have a data set like this "AA","AB","BB" and I need calculate minor allele freq and keep only these which are bigger than 5%. Have you ever done something like this?

SNP <- data.frame(SNP = c("AA","AB","BB","AA","BB","BB","AB","AA"), SNP1 = c("AA","AA","AA","BB","AA","AB","BB","AA"), SNP2 = c("AB","AB","AB","BB","AA","AA","AA","BB"))

Minor-Allele-Freq R MAF • 1.8k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 2.5 years ago by gosssheen • 0

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Your code won't work. You'll need to quote the allele strings

ADD REPLY • link 2.5 years ago by Ram 44k

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Yeah, sorry :)

ADD REPLY • link 2.5 years ago by gosssheen • 0

score 4 · Accepted Answer · 2022-05-20

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2.5 years ago

Ram 44k

You can use HardyWeinberg::maf to calculate MAF from a vector of frequencies. You can create this vector of HOM/HET/HOM-ALT frequencies using a simple table:

library(HardyWeinberg)
SNPs <- data.frame(SNP = c("AA","AB","BB","AA","BB","BB","AB","AA"), SNP1 = c("AA","AA","AA","BB","AA","AB","BB","AA"), SNP2 = c("AB","AB","AB","BB","AA","AA","AA","BB"))
table(sort(SNPs$SNP1))
AA AB BB
 5  1  2
maf(as.vector(table(sort(SNPs$SNP1))))
[1] 0.3125 # which is the same as 1-((nAA + 0.5 * nAB)/(nAA + nAB + nBB))

ADD COMMENT • link 2.5 years ago by Ram 44k

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You're the best! Thanks! :)

ADD REPLY • link 2.5 years ago by gosssheen • 0

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Please accept my answer to mark the post as solved:

upvote_bookmark_accept

ADD REPLY • link 2.5 years ago by Ram 44k