filest: Simulate data for multiple populations

In FILEST: Fine-Level Structure Simulator

Description

The output files are saved to the specified directory according to out.

Usage

filest(setting, out, thread = 1)

Arguments

setting	An absolute path to a setting file
out	An absolute path for output files
thread	A number to specify a maximum thread to be run in parallel

Details

This function takes the specific input file containing the settings for simulations. It allows multiple settings for several simulation within one file. The simulation-setting file must be a text file. The line started with "–" indicates the parameters for simulation, and the line started with "#" are comments. Empty lines are allowed in the setting file. The parameters in the setting file are listed below:

• --setting A name of setting

• --population A list that indicates the numbers of population separated by comma

• --fst A list that indicates the Fst values separated by comma. Each Fst value represents a genetic distance of that particular population and the first population. The Fst values for the first population and the second population should be the same values, otherwise they will be summed up and devided by two.

• --case A list that indicates the ratio values of cases separated by comma

• --outlier A list that indicates the logical values (0/1) whether that population are outliers, separated by comma

• --marker A number of SNPs

• --replicate A number of replicates

• --riskratio A number of replicates

• --no.case.snp A number of case SNPs

• --pc A logical value (TRUE/FALSE) whether PCs will be calculated.

• --fulloutput A logical value (TRUE/FALSE) whether all information will be exported.

Value

NULL if done successfully. NA if output directory can't be created.

Examples

#Check and run the demo from demo.filest()
demo.filest()

#Here is the code for demo.filest()
txt <- "--setting=example1\n"
txt <- paste0(txt, "--population=100,100\n")
txt <- paste0(txt, "--fst=0.01,0.01\n")
txt <- paste0(txt, "--case=0,0\n")
txt <- paste0(txt, "--outlier=0,0\n")
txt <- paste0(txt, "--marker=1000\n")
txt <- paste0(txt, "--replicate=1\n")
txt <- paste0(txt, "--riskratio=1\n")
txt <- paste0(txt, "--no.case.snp=0\n")
txt <- paste0(txt, "--pc=TRUE\n")
txt <- paste0(txt, "--missing=0\n")
txt <- paste0(txt, "--fulloutput=TRUE\n")

outdir <- file.path(tempdir())

settingfile <- file.path(outdir, "example1.txt")
fo <- file(settingfile,"w")
for (i in txt){ write(i,fo)}
close(fo)

filest(setting = settingfile, out = outdir, thread = 1)

FILEST documentation built on Jan. 25, 2021, 5:05 p.m.