calcFreqFromAd: Calculate the frequcy of Allele depth

In xuzhougeng/binmapr: Call Marker from SNP Data using Binmap

Calculate the frequcy of Allele depth

Description

Calculate the frequcy of Allele depth

Usage

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

Arguments

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

Value

matrix contains. The alt/(alt+ref) will be caculted from the allele depth

Author(s)

Zhou-geng Xu

Examples

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)

xuzhougeng/binmapr documentation built on Aug. 25, 2023, 6:44 a.m.