makefile: Create example input files

Description Usage Arguments Details Author(s) References Examples

Description

Create example files to test the package.

Usage

1
 ghap.makefile(verbose = TRUE) 

Arguments

verbose

A logical value specfying whether log messages should be printed (default = TRUE).

Details

This function downloads the following example files to the R temporary directory (requires internet connection):

human.phase
human.markers
human.samples

For details about the format of these files, see ghap.compress. The dataset was extracted from the reference phased data available at the IMPUTE2 (Howie et al., 2009) software website (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference).

The genotypes derive from the International HapMap Project Phase 3 (The International HapMap 3 Consortium, 2010), and comprise 1,011 subjects (from 11 populations) and 20,000 SNPs (randomly sampled from chromosome 2) mapped to the NCBI build 36 (hg18) assembly. The source link is (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#reference)

Author(s)

Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Marco Milanesi <marco.milanesi.mm@gmail.com>

References

B. N. Howie, P. Donnelly, and J. Marchini. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLOS Genet. 2009. 5, e1000529.

The International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations. Nature. 2010. 467, 52-58.

Examples

1
2
3
# # Copy the example data in the current working directory
# exfiles <- ghap.makefile()
# file.copy(from = exfiles, to = "./")

GHap documentation built on Oct. 23, 2020, 6:58 p.m.