calcFreqFromAd: Calculate the frequcy of AD
In binmapr: Call Marker from Snp Data using Binmap

Description Usage Arguments Value Author(s) Examples

View source: R/callGtFromAd.R

Calculate the frequcy of AD

1	calcFreqFromAd(x, min.depth = 10, max.depth = 200)

`x`	AD matrix
`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)