calcFreqFromAd | R Documentation |
Calculate the frequcy of Allele depth
calcFreqFromAd(x, min.depth = 10, max.depth = 200)
x |
a binmapr object |
min.depth |
minimum depth to infer the genotype, if depth lower than it, it will be conside as NA |
max.depth |
maximum depth to infer the genotype, if depth larger than it, it will be conside as NA |
matrix contains. The alt/(alt+ref) will be caculted from the allele depth
Zhou-geng Xu
AD <- matrix(data = c("30,1","1,30","0,0","15,15"), nrow = 2)
row.names(AD) <- c("chr1_1","chr1_100")
colnames(AD) <- c("A","B")
freq <- calcFreqFromAd(AD)
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