hapiBlockMPR: Maximum Parsimony of Recombination (MPR) for proofreading of...

In rli012/Hapi: Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells

Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypes

Description

Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypes

Usage

hapiBlockMPR(draftHap, gmtFrame, cvlink = 2, smallBlock = 100)

Arguments

draftHap	a dataframe with draft haplotype information
gmtFrame	a dataframe of raw genotype data in the framework
cvlink	a numeric value of number of cvlinks. Default is 2
smallBlock	a numeric value determining the size of small blocks that should be excluded from the draft haplotypes

Value

a dataframe of draft haplotypes after proofreading

Author(s)

Ruidong Li

Examples

ref <- rep(0,500)
alt <- rep(1,500)

gmtFrame <- 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))

gmtFrame[idx1,1] <- NA
gmtFrame[idx2,2] <- NA
gmtFrame[idx3,3] <- NA

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

draftHap <- hapiPhase(imputedFrame)

finalDraft <- hapiBlockMPR(draftHap, gmtFrame, cvlink=2, smallBlock=100)

rli012/Hapi documentation built on April 4, 2022, 8:39 p.m.