#' @export
# Runs through an example workflow
ex_function <- function(){
# Load the PheWAS package
library(simplePheWAS)
# Set the random seed so it is replicable
set.seed(2)
# Generate some example data
#ex <- generate_example(number_of_patients=2000, phenotypes_per_patient=10, code_to_enhance=c("335","764","327.1"))
# Extract the two parts from the returned list
#id.icd9.count <- ex$id.icd9.count
#genotypes <- ex$genotypes
# Or, if not generating example data, read in the data from external sources
data(testset1)
genotypes=testset1$genotypes
id.icd9.count=testset1$id.icd9.count
# Create the PheWAS code table translates the ICD9s, adds exclusions, and reshapes to a wide format
phenotypes <- create_phewas_table(id.icd9.count)
# Run the PheWAS
results <- phewas_with_bonferroni(phenotypes,genotypes)
# Print the first ten rows
print(slice(results,1:10))
# Plot the results
print(phewas_manhattan(results))
# List the significant results
results[results$bonferroni&!is.na(results$p),]
# List the top 10 results
results[order(results$p)[1:10],]
# Print the summary table
summarization_table(phenotypes, genotypes, results)
}
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