hapiAssembleEnd {Hapi} | R Documentation |
Assembly of haplotypes in regions at the end of a chromosome
Description
Assembly of haplotypes in regions at the end of a chromosome
Usage
hapiAssembleEnd(gmt, draftHap, consensusHap, k = 300)
Arguments
gmt |
a dataframe of genotype data of gamete cells |
draftHap |
a dataframe with draft haplotype information |
consensusHap |
a dataframe of the consensus haplotype information |
k |
a numeric value for the number of hetSNPs that will be combined with markers beyond the framework for assembly. Default is 300 |
Value
a dataframe containing phased haplotypes
Author(s)
Ruidong Li
Examples
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 <- data.frame(hap1=rep(0,500),hap2=rep(1,500),
total=rep(5,500),rate=rep(1,500),
confidence=rep('F',500),
stringsAsFactors = FALSE)
rownames(consensusHap) <- seq_len(500)
consensusHap <- hapiAssembleEnd(gmt = gmtDa, draftHap = finalDraft,
consensusHap = consensusHap, k = 300)
[Package Hapi version 0.0.3 Index]