hapiCVCluster: Filter out hetSNPs in potential complex regions

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

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)

Jialab-UCR/Hapi documentation built on May 30, 2019, 11:41 a.m.