snp_simuPheno: Simulate phenotypes

Description Usage Arguments Value

View source: R/simu-pheno.R

Description

Simulate phenotypes using a linear model. When a prevalence is given, the liability threshold is used to convert liabilities to a binary outcome. The genetic and environmental liabilities are scaled such that the variance of the genetic liability is equality the requested heritability, and the variance of the total liability is 1.

Usage

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snp_simuPheno(
  G,
  h2,
  M,
  K = NULL,
  ind.row = rows_along(G),
  ind.possible = cols_along(G),
  effects.dist = c("gaussian", "laplace"),
  ncores = 1
)

Arguments

G

A FBM.code256 (typically <bigSNP>$genotypes).
You shouldn't have missing values. Also, remember to do quality control, e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.

h2

Heritability.

M

Number of causal variants.

K

Prevalence. Default is NULL, giving a continuous trait.

ind.row

An optional vector of the row indices (individuals) that are used. If not specified, all rows are used.
Don't use negative indices.

ind.possible

Indices of possible causal variants.

effects.dist

Distribution of effects. Either "gaussian" (the default) or "laplace".

ncores

Number of cores used. Default doesn't use parallelism. You may use nb_cores.

Value

A list with 3 elements:


bigsnpr documentation built on June 3, 2021, 5:12 p.m.