## ----eval = FALSE-------------------------------------------------------------
# install.packages("RapidoPGS")

## ----eval=FALSE---------------------------------------------------------------
# if (!requireNamespace("remotes", quietly = TRUE))
#     install.packages("remotes")
# remotes::install_github("GRealesM/RapidoPGS")

## ----message=FALSE, warning = FALSE-------------------------------------------
library(RapidoPGS)

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

## ----eval=FALSE---------------------------------------------------------------
# 
# dir.create("ukbb")  # Or whatever you like
# download.file("https://ndownloader.figshare.com/articles/13034123/versions/3", destfile="ukbb/LD_ukbb.zip", mode="wb")
# unzip(zipfile="ukbb/LD_ukbb.zip", exdir="ukbb/")
# 

## ----eval=FALSE---------------------------------------------------------------
# ds <- michailidou19

## ----eval=FALSE---------------------------------------------------------------
# model.LDmat <- rapidopgs_multi(ds, LDmatrices = "ukbb", N = 256123, build = "hg19", trait="cc")

## ----eval=FALSE---------------------------------------------------------------
# model.refpanel <- rapidopgs_multi(ds, reference = "ref-data",  N = 256123, build = "hg19", trait="cc", ncores=8)