Phenome Wide Association Studies (PheWAS)

Documentation for package ‘PheWAS’ version 0.12

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PheWAS-package	PheWAS analysis methods
addPhecodeInfo	Add phecode descriptions and group information to existing data.
addPhewasDescription	Add phecode descriptions and group information to existing data.
addPhewasGroups	Add phecode descriptions and group information to existing data.
createPhewasTable	Creates a phenotype table from id, ICD-9 (or phecode, etc), count data.
gender_restriction	Data frame containing potential gender-restricted phewas codes.
generateExample	Generate example data for PheWAS
mapICD9ToPhecodes	Map ICD9 codes to phecodes
mapICD9toPheWAS	Map ICD9 codes to phecodes
mapPhecodesToExclusions	Map phecodes to their exclusions
mapPheWAStoExclusions	Map phecodes to their exclusions
phecode_exclude	Dataframe containing phewas code mappings to their exclusions
pheinfo	Data frame containing phecode information.
phemap	Dataframe containing phecode mappings.
phenotypeManhattan	Plotting methods for PheWAS results, phenotype association studies, or generic phenotype values
phenotypePlot	Plotting methods for PheWAS results, phenotype association studies, or generic phenotype values
PheWAS	PheWAS analysis methods
phewas	Function to perform a PheWAS analysis
PheWAS-defunct	Defunct methods in the PheWAS package
phewasDT	Wrapper to create a browsable datatable
phewasManhattan	Plotting methods for PheWAS results, phenotype association studies, or generic phenotype values
phewasMeta	Perform meta-analysis of PheWAS results
phewasMetaModels	Perform meta-analysis of PheWAS results
phewas_ext	Function to perform a PheWAS analysis with multiple methods
PheWAS_Plotting	Plotting methods for PheWAS results, phenotype association studies, or generic phenotype values
plinkPhewasExport	Export a table for PheWAS analysis in plink
restrictPhecodesByGender	Add PheWAS code descriptions to existing data.