create_artificial_data: Create an Artificial eQTL Data Set

In ACMEeqtl: Estimation of Interpretable eQTL Effect Sizes Using a Log of Linear Model

Description

Create artificial genotype, gene expression, covariate, and gene/SNP location data sets.

Usage

create_artificial_data(
    nsample,
    ngene = 5000,
    nsnp = 500e+03,
    ncvrt = 10,
    minMAF = 0.2,
    saveDir = ".",
    returnData = FALSE,
    savefmat = FALSE,
    savetxt = FALSE,
    verbose = TRUE)

Arguments

nsample	Number of samples.
ngene	Number of genes.
nsnp	Number of SNPs.
ncvrt	Number of covariates.
minMAF	Minimum minor allele frequency of generated SNPs.
saveDir	Directory for the output.
returnData	Set to TRUE to return generated data in an R list.
savefmat	Save generated data in filematrix format. This format is used by multithreadACME.
savetxt	Save generated data in text format. This format is used by Matrix eQTL MatrixEQTL.
verbose	Set to TRUE to indicate progress.

Value

The function generates the following text files and/or filematrices:

cvrt	Covariates
gene	Gene expression
snps	SNPs (genotype)
gene_loc	Gene locations
snps_loc	SNP locations
etas	SNP effect on the genes

Author(s)

Andrey A Shabalin [e-mail], John Palowitch

References

The manuscript is available at: http://onlinelibrary.wiley.com/doi/10.1111/biom.12810/full

See Also

For package overview and code examples see the package vignette via:
browseVignettes("ACMEeqtl")

For fast testing of all local gene-SNP pairs (local eQTL) see multithreadACME.

Examples

z = create_artificial_data(
		nsample = 10,
		ngene = 51,
		nsnp = 501,
		ncvrt = 1,
		minMAF = 0.2,
		returnData = TRUE,
		savefmat = FALSE,
		savetxt = FALSE,
		verbose = TRUE)
    
names(z)

ACMEeqtl documentation built on May 2, 2019, 4:03 p.m.