hapiCVCluster {Hapi}

Filter out hetSNPs in potential complex regions

Description

Filter out hetSNPs in potential complex regions

Usage

hapiCVCluster(draftHap, minDistance = 1e+06, cvlink = 2)

Arguments

draftHap

a dataframe with draft haplotype information

minDistance

a numeric value of the distance between two genomic positions with cv-links. Default is 1000000

cvlink

a numeric value of number of cvlinks. Default is 2

Value

a dataframe of regions to be filtered out

Author(s)

Ruidong Li

Examples

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

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

draftHap <- hapiPhase(imputedFrame)
cvCluster <- hapiCVCluster(draftHap = draftHap, cvlink=2)