callGtFromAd: call genotype from AD

In binmapr: Call Marker from Snp Data using Binmap

Description

call genotype from AD

Usage

callGtFromAd(x, min.depth = 10, max.depth = 200, low = 0.2,
  high = 0.8)

Arguments

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
low	threshold to infer one parent, encoded as 0
high	threshold to infer another parent, encoded as 2

Value

matrix contains. The allele depth will convet to genotype

Author(s)

Zhougeng 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")
geno <- callGtFromAd(AD)

binmapr documentation built on Oct. 30, 2019, 12:14 p.m.