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

In Hapi: Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

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)

Hapi documentation built on May 2, 2019, 6:52 a.m.