savePheno: Save final phenotype and phenotype components.

In HannahVMeyer/PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models

Description

savePheno saves simulated phenotypes and their components, model setup parameters and variance components to the specified directories. Requires a simulatedData list which is the output of runSimulation.

Usage

savePheno(
  simulatedData,
  directory,
  format = ".csv",
  outstring = "",
  saveIntermediate = TRUE,
  intercept_gemma = TRUE,
  verbose = TRUE
)

Arguments

simulatedData	Named list of i) dataframe of proportion of variance explained for each component (varComponents), ii) a named list with the final simulated phenotype components (phenoComponentsFinal), iii) a named list with the intermediate simulated phenotype components (phenoComponentsIntermediate), iv) a named list of parameters describing the model setup (setup) and v) a named list of raw components (rawComponents) used for genetic effect simulation (genotypes and/or kinship); obtained from runSimulation
directory	Absolute path (no tilde expansion) to parent directory [string] where simulated data should be saved [needs user writing permission]
format	Vector of format name(s) [string] specifying the output format; multiple output formats can be requested. Options are: plink, bimbam, snptest, gemma, limmbo, csv or rds. For information on format see details. In orde to save intermediate phenotype components, at least one of csv or rds need to be specified. plink/bimbam/snptest will only save final phenotype/genotype, kinship and covariate data.
outstring	Optional name [string] of subdirectory (in relation to directory) to save set-up dependent simulation results; if set to NULL, subdirectory named by NrSamples, NrSNPs, genetic Model and noise Model and genVar is created.
saveIntermediate	[bool] If TRUE, intermediate phenotype components such as shared and independent effect components are saved.
intercept_gemma	[boolean] When modeling an intercept term in gemma, a column of 1's have to be appended to the covariate files. Set intercept_gemma to TRUE to include a column of 1's in the output; only used when "gemma" %in% format
verbose	[boolean]; If TRUE, progress info is printed to standard out

Value

Path [string] to final output directory. If outstring is NULL, this directory will be a subdirectory of the input directory.

Examples

simulatedPhenotype <- runSimulation(N=100, P=5, cNrSNP=10,
genVar=0.2, h2s=0.2, phi=1)
## Not run: 
outputdir <- savePheno(simulatedPhenotype, directory=tempdir(),  
outstring="Data_simulation", format=c("csv", "plink"))
## End(Not run)

HannahVMeyer/PhenotypeSimulator documentation built on July 19, 2021, 7:41 a.m.