read.simu.pars: Read parameters

In SimPhe: Tools to Simulate Phenotype(s) with Epistatic Interaction

Description

Read file specifying the simulation parameters.

Usage

read.simu.pars(file = NULL, ...)

Arguments

file	the file of parameters settings
...	not used

Details

File format: please follow the example of the simupars.txt file found in the inst/extdata/ directory of the package (run
system.file("extdata", "simupars.txt", package="SimPhe")
to see the full path), blank lines are ignored. The file consists of three or four blocks for each phenotype: mean, main, epistasis, and (optionally) heritability. Each block is started by a line of the form '[blockname]' followed by the parameters for the block, e.g., for thefirst phenotype,

[P1mean]

mean

β_0: coefficient parameter of "basic" genetic effects in Gij = β_0 + ∑(β_Gwt*wtij), t in (1, 2, ..., 8).

[P1main]

SNP

SNP name

additive

coefficient of additive effect

dominance

coefficient of dominance effect

[P1epistasis]

SNPA

first SNP name

SNPB

second SNP name

additive_additive

coefficient for additive-additive interaction

additive_dominance

coefficient for additive-dominance interaction

dominance_additive

coefficient for dominance-additive interaction

dominance_dominance

coefficient for dominance-dominance interaction

[P1heritability]

heritability

expected heritability

For each block the expected columns and the respective menaings are given. Similar blocks need to be provided for the other phenotype(s): "[P2mean]", "[P2main]", "[P2epistasis]", and so on.

Value

a list of simulation parameters. One element per block of file. Each element is a dataframe with SNP names and model parameters

Author(s)

Beibei Jiang [e-mail] and Benno Pütz [e-mail]

Examples

# simulation parameters:
fpar.path <- system.file("extdata", "simupars.txt", package="SimPhe")


# pars <- read.simu.pars(fpar.path)

SimPhe documentation built on May 1, 2019, 9:10 p.m.