hap2plink: Convert haplotype allele counts to PLINK binary

In GHap: Genome-Wide Haplotyping

Convert haplotype allele counts to PLINK binary

Description

This function takes a HapGenotypes matrix (as generated with the ghap.haplotyping function) and converts it to PLINK binary (bed/bim/fam) format.

Usage

ghap.hap2plink(object, outfile)

Arguments

object	A GHap.haplo object.
outfile	A character value specifying the name used for the .bed, .bim and .fam output files.

Details

The returned file mimics a standard PLINK (Purcell et al., 2007; Chang et al., 2015) binary file (bed/bim/fam), where HapAllele counts 0, 1 and 2 are recoded as NN, NH and HH genotypes (N = NULL and H = haplotype allele), as if HapAlleles were bi-alelic markers. This codification is acceptable for any given analysis relying on SNP genotype counts, as long as the user specifies that the analysis should be done using the H character as reference for counts. You can specify reference alleles using the .tref file in PLINK with the –reference-allele command. This is desired for very large datasets, as softwares such as PLINK and GCTA (Yang et al., 2011) have faster implementations for regression, principal components and kinship matrix analyses. The name for each pseudo-marker is composed by a concatenation (separated by "_") of block name, start, end and haplotype allele identity. Pseudo-marker positions are computed as (start+end)/2.

Author(s)

Yuri Tani Utsunomiya <[e-mail]>
Marco Milanesi <[e-mail]>

References

C. C. Chang et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015. 4, 7.

S. Purcell et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 2007. 81, 559-575.

J. Yang et al. GCTA: A tool for genome-wide complex trait analysis. Am. J. Hum. Genet. 2011. 88, 76-82.

Examples

# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy phase data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "phase",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# ### RUN ###
# 
# # Load data
# phase <- ghap.loadphase("example")
# 
# # Generate blocks of 5 markers
# blocks <- ghap.blockgen(phase, windowsize = 5,
#                         slide = 5, unit = "marker")
# 
# # Haplotyping
# ghap.haplotyping(phase = phase, blocks = blocks, outfile = "example",
#                  binary = T, ncores = 1)
# 
# # Load haplotype genotypes using prefix
# haplo <- ghap.loadhaplo("example")
# 
# ### RUN ###
# 
# # Convert to plink
# ghap.hap2plink(haplo, outfile = "example")

GHap documentation built on July 2, 2022, 1:07 a.m.