hapiFilterError: Filter out hetSNPs with potential genotyping errors

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

Description

Filter out hetSNPs with potential genotyping errors

Usage

hapiFilterError(gmt, hmm = NULL)

Arguments

gmt	a dataframe of genotype data of gamete cells
hmm	a list containing probabilities of a HMM. Default is NULL

Value

a dataframe of genotype data of gamete cells

Author(s)

Ruidong Li

Examples

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

gmt <- data.frame(gmt1=ref, gmt2=alt, gmt3=ref,
    gmt4=ref, gmt5=c(alt[1:250], ref[251:500]),
    stringsAsFactors = FALSE)
    
idx <- sort(sample(seq_len(500), 10, replace = FALSE))
gmt[idx,1] <- 1

gmtDa <- hapiFilterError(gmt = gmt)

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