Fine-Level Structure Simulator

Description

A population genetic simulator, which is able to generate synthetic datasets for single-nucleotide polymorphisms (SNP) for multiple populations. The genetic distances among populations can be set according to the Fixation Index (Fst). This tool is able to simulate outlying individuals and missing SNPs can be specified. For Genome-wide association study (GWAS), disease status can be set in desired level according risk ratio.

Details

The R package FILEST requires KRIS and rARPACK.

Here is the list of functions in the R package FILEST:

• cbind_bigmatrix

• create.template.setting

• demo.filest

• filest

• rbind_bigmatrix

Author(s)

Maintainer: Kridsadakorn Chaichoompu kridsadakorn@biostatgen.org

Authors:

• Kristel Van Steen

• Fentaw Abegaz

See Also

Useful links:

• https://gitlab.com/kris.ccp/filest

• Report bugs at https://gitlab.com/kris.ccp/filest/-/issues

Combind two matrices by column for big data, internally used for parallelization

Description

Combind two matrices by column for big data, internally used for parallelization

Usage

cbind_bigmatrix(a, b)

Arguments

Value

The combined matrix by column

See Also

rbind_bigmatrix

Examples

X <- matrix(c(1,2,0,1,2,2,1,2,0,0,1,2,1,2,2,2),ncol=4)
Y <- matrix(c(2,1,1,0,1,0,0,1,1,2,2,0,0,1,1,0),ncol=4)
Z <- cbind_bigmatrix(X,Y)
print(Z)

Create a template for a setting file of function filest

Description

Create a template for a setting file of function filest

Usage

create.template.setting(out.file, no.setting = 1)

Arguments

Value

An output directory if suggessfully created. Null if a setting file can't be created.

Examples

#Create 2 simulated settings

output <- file.path(tempdir(),"example_setting.txt")
res <- create.template.setting(out.file = output, no.setting = 2)
print(res)

Demonstration the filest function

Description

This function generates the setting file and demonstrate how to use filest.

Usage

demo.filest()

Value

The output directory

Examples

#To run this function, simply call demo.filest()
demo.filest()

Simulate data for multiple populations

Description

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

Usage

filest(setting, out, thread = 1)

Arguments

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)

Combind two matrices by row for big data, internally used for parallelization

Description

Combind two matrices by row for big data, internally used for parallelization

Usage

rbind_bigmatrix(a, b)

Arguments

Value

The combined matrix by row

See Also

cbind_bigmatrix

Examples

X <- matrix(c(1,2,0,1,2,2,1,2,0,0,1,2,1,2,2,2),ncol=4)
Y <- matrix(c(2,1,1,0,1,0,0,1,1,2,2,0,0,1,1,0),ncol=4)
Z <- rbind_bigmatrix(X,Y)
print(Z)