genhaps: Generate haplotypes

In chr1swallace/snpHaps: EM haplotype inference and association testing through multiple imputation

Description

Write a snpStats object to file, and use snphap to phase with multiple imputation

Usage

genhaps(data, slist = colnames(data), snps, samples, A1 = "allele.A",
  A2 = "allele.B", cols.copy = character(0), f.in = "snphap/haps.in",
  redo = FALSE)

Arguments

data	snpStats object
slist	snp list
snps	snps dataframe with columns "allele.A", "allele.B" denoting alleles
samples	samples dataframe
A1	colname of allele 1 in snps
A2	colname of allele 2 in snps
cols.copy	columns to be copied to resulting phased object
f.in	filename for snphap input (will be overwritten)
redo	set to TRUE to regenerate snphap output regardless of whether it exists

Value

data.frame containing the best phased haplotypes

Author(s)

Chris Wallace

chr1swallace/snpHaps documentation built on May 13, 2019, 6:20 p.m.