doc/install.md

In richelbilderbeek/plinkr: Interface to PLINK

Installation

This page explains how to:

• Install plinkr
• Install all PLINK versions
• Install a specific PLINK version
  • Install PLINK v1.7
  • Install PLINK v1.9
  • Install PLINK v2.0
• Do a custom PLINK installation
  • Install the PLINK versions elsewhere
  • Install the PLINK versions in custom (sub)folders

Install plinkr

plinkr is not on CRAN yet. To install plinkr:

library(remotes)
install_github("richelbilderbeek/plinkr")

This assumes you have the remotes package installed.

Install pgenlibr

remotes::install_github("chrchang/plink-ng/2.0/pgenlibr")

Install all PLINK versions

plinkr uses multiple version of PLINK. To install them all:

library(plinkr)
install_plinks()

Use get_plink_versions() to see which versions are supported.

Install a specific PLINK version

plinkr works with multiple versions of plink by default. It is possible to only install a single version:

• Install PLINK v1.7
• Install PLINK v1.9
• Install PLINK v2.0

Use get_plink_versions() to see which versions are supported.

Install PLINK v1.7

To install only PLINK v1.7:

library(plinkr)
plink_options <- create_plink_v1_7_options()
install_plink(plink_options = plink_options)

Use the same ´plink_options´ when calling PLINK, to call this version of PLINK.

Install PLINK v1.9

To install only PLINK v1.9:

library(plinkr)
plink_options <- create_plink_v1_9_options()
install_plink(plink_options = plink_options)

Use the same ´plink_options´ when calling PLINK, to call this version of PLINK.

Install PLINK v2.0

To install only PLINK v2.0:

library(plinkr)
plink_options <- create_plink_v2_0_options()
install_plink(plink_options = plink_options)

Use the same ´plink_options´ when calling PLINK, to call this version of PLINK.

Do a custom PLINK installation

• Install the PLINK versions elsewhere
• Install the PLINK versions in custom (sub)folders

Install the PLINK versions elsewhere

To install all PLINK versions in a different folder, specify that folder in the plink_optionses argument of install_plinks:

install_plinks(create_plink_optionses(plink_folder = "my_folder"))

This will create the multiple versions if PLINK in the default subfolders.

Install the PLINK versions in custom (sub)folders

To install the different PLINK versions in different folder, specify those folders in the plink_optionses argument of install_plinks:

plink_optionses <- list(
  create_plink_v1_7_options(plink_folder = "my_folder"),
  create_plink_v1_9_options(plink_folder = "another_folder")
)

install_plinks(plink_optionses)

This will create the multiple versions of PLINK, each in its own custom (sub)folder.

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.