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remove problematic whitespace in example #1

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remove problematic whitespace in example #1

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19 changes: 10 additions & 9 deletions phecodeX_PheWAS_example_R_script.txt
100644 → 100755
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
library(PheWAS)
set.seed(1)
 

## make sure you add the right path!
phecodeX_labels = read.csv('phecodeX_R_labels.csv')
phecodeX_rollup_map = read.csv('phecodeX_R_rollup_map.csv')
phecodeX_map = read.csv('phecodeX_R_map.csv')
phecodeX_sex = read.csv('phecodeX_R_sex.csv')
 

#Generate some example data
ex=generateExample()

Expand All @@ -21,16 +21,17 @@ id.sex=ex$id.sex
#Note the vocabulary.map and rollup.map are set to
#phecodeX files
phenotypesX = createPhenotypes(id.vocab.code.count,
                            aggregate.fun=sum, id.sex=id.sex,
                            vocabulary.map=phecodeX_map,
                            rollup.map=phecodeX_rollup_map, sex.restriction=phecodeX_sex)

aggregate.fun=sum, id.sex=id.sex,
vocabulary.map=phecodeX_map,
rollup.map=phecodeX_rollup_map,
sex.restriction=phecodeX_sex)

#Combine the data
data = inner_join(inner_join(phenotypesX,genotypes),id.sex)
 

#Run the PheWAS
results = phewas_ext(data,phenotypes=names(phenotypesX)[-1], genotypes=c("rsEXAMPLE"), covariates=c("sex"))
 

## Add phecode_labels
results_annotated = merge(phecodeX_labels, results, by='phenotype')

Expand All @@ -39,4 +40,4 @@ phenotypeManhattan(results_annotated,
title="My Example PheWAS Manhattan Plot",
annotate.phenotype.description=T,
sort.by.category.value=F, x.group.labels=T,
use.color=T)
use.color=T)