1 | RadPheWAS-package(x)
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x |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | #Load the PheWAS package
library(RadPheWAS)
#Set the random seed so it is replicable
set.seed(1)
#Generate some example data
ex=generate_example()
#Extract the two parts from the returned list
id.icd9.count=ex$id.icd9.count
genotypes=ex$genotypes
#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(phenotypes,genotypes,cores=1,
significance.threshold=c("bonferroni"))
#Plot the results
phewasManhattan(results, annotate.angle=0,
title="My Example PheWAS Manhattan Plot")
#Add PheWAS descriptions
results_d=addPhewasDescription(results)
#List the significant results
results_d[results_d$bonferroni&!is.na(results_d$p),]
#List the top 10 results
results_d[order(results_d$p)[1:10],]
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