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Assemble the consensus high-resolution haplotypes
hapiAssemble(gmt, draftHap, keepLowConsistency = TRUE,
consistencyThresh = 0.85)
a dataframe of genotype data of gamete cells
a dataframe with draft haplotype information
logical, if low-consistent gamete cells should be kept
a numeric value of the threshold determining low-consistent gamete cells compared with the draft haplotype. Default is 0.85
a dataframe containing phased haplotypes
# NOT RUN {
finalDraft <- rep(0,500)
names(finalDraft) <- seq_len(500)
ref <- rep(0,500)
alt <- rep(1,500)
gmtDa <- data.frame(gmt1=ref, gmt2=alt, gmt3=ref,
gmt4=ref, gmt5=c(alt[1:250], ref[251:500]),
stringsAsFactors = FALSE)
idx1 <- sort(sample(seq_len(500), 30, replace = FALSE))
idx2 <- sort(sample(seq_len(500), 30, replace = FALSE))
idx3 <- sort(sample(seq_len(500), 30, replace = FALSE))
gmtDa[idx1,1] <- NA
gmtDa[idx2,2] <- NA
gmtDa[idx3,3] <- NA
consensusHap <- hapiAssemble(draftHap = finalDraft, gmt = gmtDa)
# }
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