createPhewasTable: Creates a phenotype table from id, ICD-9 (or phecode, etc),...

In PheWAS/PheWAS: Phenome Wide Association Studies (PheWAS)

Creates a phenotype table from id, ICD-9 (or phecode, etc), count data.

Description

Deprecated, please see createPhenotypes. This function takes a data frame with three columns: id, icd9 codes, and counts. It returns a wide table with ICD-9 codes translated into phewas codes. It can optionally use the PheWAS exclusion criteria. Results can be formatted as true/false for a specified threshold or as summed continuous counts.

Usage

createPhewasTable(id.icd9.count, min.code.count = 2, add.exclusions = T,
  translate = T, aggregate.fun = sum, id.gender)

Arguments

id.icd9.count	Data frame with three columns: id, ICD-9 character string, and count.
min.code.count	The minimum code count to be considered a case. NA results in a continuous output.
add.exclusions	Apply PheWAS exclusions to phecodes.
translate	Should the input be translated to phecodes? This requires ICD-9 code input.
aggregate.fun	Aggregate function for duplicated phenotypes (phecodes, etc) in an individual.
id.gender	If supplied, restrict the phecodes by gender. This should be a data frame with the first column being the id and the second the gender, "M" or "F", of the individual. Individuals with any other specification will have all gender specific phenotypes set to NA.

Details

By default, this function returns a wide format data frame with boolean phenotypes suitable for PheWAS analysis. Specifying a min.code.count=NA will permit continuous code count phenotypes.

The default exclusions can be skipped with add.exclusions=F. In conjuntion with translate=F (and optionally adjusting min.code.count and aggregate.fun), one can use this function as a simple reshaping wrapper.

Value

A data frame. The first column contains the supplied id for each individual (preserving the name of the original column). The following columns are all present phewas codes. They contain T/F/NA for case/control/exclude or continuous/NA if min.code.count was NA.

Author(s)

Robert Carroll Laura Wiley

Examples

#Simple example
id_icd9_count=data.frame(id=c(1,2,2,2,3),icd9=c("714","250.11","714.1","714","250.11"),
  count=c(1,5,1,1,0))
createPhewasTable(id_icd9_count)

#Complex example
ex=generateExample(n=500,hit="335")
#Extract the icd9 data
id.icd9.count=ex$id.icd9.count
#Create the phecode table for a PheWAS
phenotypes=createPhewasTable(id.icd9.count)
phenotypes[1:10,1:10]

PheWAS/PheWAS documentation built on July 3, 2023, 3:40 p.m.