In richelbilderbeek/plinkr: Interface to PLINK

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(plinkr)

With create_demo_assoc_qt_data one can get simulated/ideal data with known relations between genotype and phenotype. assoc_qt can directly use the created data to do a quantitative trait association analysis.

This vignette shows the versatility of create_demo_assoc_qt_data, by calling it in multiple different ways. The output is left as-is, i.e. no pretty-printing.

One trait

Random

create_demo_assoc_qt_data(
  traits = create_random_trait()
)

A random trait is a trait in which there is no relationship between genotype. In this case, the phenotype is randomly and uniformly distributed between zero and one.

Random with more individuals

create_demo_assoc_qt_data(
  traits = create_random_trait(),
  n_individuals = 5
)

You can specify the number of individuals that are created. The rarer the alleles you are looking for, the more individuals you'll need :-)

Random for a MAF of 0.1

create_demo_assoc_qt_data(
  traits = create_random_trait(mafs = 0.1)
)

By default, the minor allele frequency is set to a high value, as this is most useful when demonstrating an effect. To investigate an allele that is rare, one can specify the MAF of each allele. Don't forget to increase the number of individuals!

Random for a tri-allelic trait

create_demo_assoc_qt_data(
  traits = create_random_trait(mafs = c(0.2, 0.1))
)

Usually SNPs are bi-allelic, with only two different nucleotides present in the genetic dataset. Sometimes, however, there is a tri-allelic trait. You can simulate such a tri-allelic trait by specifying both the MAF and the frequency of the even rarer nucleotide.

Note that PLINK does not handle tri-allelic traits and will only work on the common and the minor allele.

Random for a quad-allelic trait

create_demo_assoc_qt_data(
  traits = create_random_trait(mafs = c(0.3, 0.2, 0.1))
)

DNA has four nucleotides, so SNPs can be quad-allelic as well. You can simulate such a quad-allelic trait by specifying the allele frequencies of the rarer nucleotides.

Note that PLINK does not handle tri-allelic traits and will only work on the common and the minor allele.

Additive

create_demo_assoc_qt_data(
  traits = create_additive_trait()
)

A additive trait is a trait in which the phenotype is linearily (and perfectly) determined by the genotype. The homozygotes of the common allele have the lowest phenotypic value, the homozygotes of the rare allele have the heighest, where the heterozygotes are exactly in between.

See ?calc_additive_phenotype_values for the exact calculation.

Epistatic

create_demo_assoc_qt_data(
  traits = create_epistatic_trait()
)

Two traits

The same trait twice

create_demo_assoc_qt_data(
  traits = rep(list(create_random_trait()), 2)
)

The same trait twice, with different MAFs

create_demo_assoc_qt_data(
  traits = list(
    create_random_trait(mafs = 0.2),
    create_additive_trait(mafs = 0.4)
  )
)

Two different traits

create_demo_assoc_qt_data(
  traits = list(
    create_random_trait(),
    create_additive_trait()
  )
)

More traits

create_demo_assoc_qt_data()

Cleanup

clear_plinkr_cache()

check_empty_plinkr_folder()

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