#' Generate test data
#'
#' Generates test data files, mainly for debugging and testing.
generate_test_data <- function() {
# Create sample names
test_sample_names <- lapply(seq(1, 30, 1), function(i) {
paste("sample", i, sep="")
})
# Load default data.
phpo <- leqtar::gencode_position
gepo <- leqtar::gepo
#Genrate genotype data.
snps <- sample(gepo$snp, 30)
snps_geno <- sapply(snps, function(snp) {
pattern = stringi::stri_rand_strings(1, 2, pattern = "[ACTG]")
data.frame(snp=stringi::stri_rand_strings(30, 2, pattern = paste("[",pattern,"]", sep="") ) )
})
genotype_test_data <- t(data.frame(snps_geno))
colnames(genotype_test_data) <- test_sample_names
rownames(genotype_test_data) <- snps
genotype_test_locations <- gepo[which(gepo$snp %in% snps),]
colnames(genotype_test_locations) <- c("snps", "chr", "pos")
# Generate phenotype data.
phenotype_genes <- sample(phpo$geneid, 50)
phenotype_test_data <- matrix(rbinom(10*300, 10, .5), ncol=30, nrow=50)
rownames(phenotype_test_data) <- phenotype_genes
colnames(phenotype_test_data) <- test_sample_names
phenotype_test_locations <- phpo[which(phpo$geneid %in% phenotype_genes),]
# Generate covariates.
covariate_test_data <- t(data.frame( replicate(30, sample(18:75, 1, rep=T) ), replicate(30, sample(0:1, 1, rep=T) ) ))
colnames(covariate_test_data) <- test_sample_names
rownames(covariate_test_data) <- c("age", "gender")
# Save data.
devtools::use_data(genotype_test_data, overwrite = T)
devtools::use_data(genotype_test_locations, overwrite = T)
devtools::use_data(phenotype_test_data, overwrite = T)
devtools::use_data(phenotype_test_locations, overwrite = T)
devtools::use_data(covariate_test_data, overwrite = T)
# save(genotype_test_data, file="~/git/leqtar/data/genotype_test_data.RData", compress = "xz")
# save(phenotype_test_data, file="~/git/leqtar/data/phenotype_test_data.RData", compress = "xz")
# save(covariate_test_data, file="~/git/leqtar/data/covariate_test_data.RData", compress = "xz")
# save(genotype_test_locations, file="~/git/leqtar/data/genotype_test_locations.RData", compress = "xz")
# save(phenotype_test_locations, file="~/git/leqtar/data/phenotype_test_locations.RData", compress = "xz")
}
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