create_1000G: Download 1000 Genomes Phase III panel

In GRealesM/RapidoPGS: A Fast and Light Package to Compute Polygenic Risk Scores

Download 1000 Genomes Phase III panel

Description

create_1000G downloads and gets 1000 Genomes Phase III panel (hg19) in PLINK format, and apply quality control for being used to compute PGS using rapidopgs_multi. Given the size of the files, running this function can take long, depending on broadband speed and server status. We also recommend to ensure that there is at least 60GB free space available in disk.

Usage

create_1000G(
  directory = "ref-data",
  remove.related = TRUE,
  qc.maf = 0.01,
  qc.hwe = 1e-10,
  qc.geno = 0,
  autosomes.only = TRUE
)

Arguments

directory	a string indicating the directory to download the panel
remove.related	a logical stating if related individuals should be removed. Default TRUE.
qc.maf	a numeric to set the MAF threshold for variants to be removed. DEFAULT 0.01
qc.hwe	a numeric indicating the threshold for Hardy-Weinberg exact test p-value, below which variants will be removed. DEFAULT 1e-10.
qc.geno	a numeric to set maximum missing call rates for variants. DEFAULT = 0.
autosomes.only	If FALSE, it will include X and Y chromosomes, too.

Value

bed, fam and bim files for each chromosome in the chosen directory.

Author(s)

Guillermo Reales

Examples

## Not run: 
create_1000G()

## End(Not run)

GRealesM/RapidoPGS documentation built on Oct. 15, 2023, 2:43 p.m.