hapiIdentifyCV {Hapi}

Indentify crossovers in gamete cells

Description

Indentify crossovers in gamete cells

Usage

hapiIdentifyCV(hap, gmt, hmm = NULL)

Arguments

hap

a dataframe of the two haplotypes

gmt

a dataframe of genotype data of gamete cells

hmm

a list containing probabilities of a HMM. Default is NULL

Value

a dataframe containing crossover information in each gamete cell

Author(s)

Ruidong Li

Examples

ref <- sample(c('A','T'),500, replace=TRUE)
alt <- sample(c('C','G'),500, replace=TRUE)

hap <- data.frame(hap1=ref, hap2=alt, stringsAsFactors = FALSE)
rownames(hap) <- seq_len(500)

gmt <- data.frame(gmt1=ref, gmt2=alt, gmt3=ref,
    gmt4=ref, gmt5=c(alt[1:250], ref[251:500]),
    stringsAsFactors = FALSE)
    
cvOutput <- hapiIdentifyCV(hap=hap, gmt=gmt)