doc/faq.md

In richelbilderbeek/plinkr: Interface to PLINK

FAQ

• Installation
• General
• Technical

Installation

See install.md

General

On which operating systems can I run plinkr?

On Linux and Windows.

plinkr is tested to work on Linux by GitHub Actions, and tested to work on Windows by AppVeyor.

Why is this package not on CRAN?

Because no real users have yet tested it, except me.

When it moves to CRAN, the install and uninstall functions will move to a non-CRAN package, as these functions violate CRAN policy.

Technical

Which PLINK versions are supported?

• PLINK v1.7
• PLINK v1.9
• PLINK2 v2.0

Can plinkr handle SNPs with three or four alleles?

No. PLINK cannot, so plinkr cannot.

How can I use a version of PLINK I have installed elsewhere?

The create_custom_plink_options allows to do so. If the PLINK executable can be found at my_plink_path/plink3.mp4, create a plink_options as such:

plink_options <- create_custom_plink_options("my_plink_path/plink3.mp4")

This plink_options can be used in all functions that call PLINK, for example:

get_plink_version(plink_options)

Are there packages like plinkr?

Yes, there are R packages that have a subset of the plinkr functionality

Why don't you use packages with the (subset of) the plinkr functionality?

I do if I can, if I dare rely on those packages.

These are package(s) I dare rely on:

• genio

These are package(s) I dare not rely on:

• quartzbio/plinker_pkg: discontinued since 2018

What is unique about plinkr?

• It can use multiple version of PLINK and PLINK2, allowing for a direct comparison
• It can simulate data
• It follows all (if not, let me know) quality guidelines as described im the literature, specifically the Tidyverse guidelines

What about the logo

I searched DuckDuckGo Image Search for a transparent public domain image using the search term pink:

https://duckduckgo.com/?q=pink&t=ffab&iar=images&iaf=type%3Atransparent%2Clicense%3APublic%2Ccolor%3AMonochrome&iax=images&ia=images&iai=https%3A%2F%2Fcdn.pixabay.com%2Fphoto%2F2018%2F04%2F22%2F22%2F03%2Fsilhouette-3342563_640.png

I modified the image in KolorPaint and added the R logo.

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