Files in hugheylab/phers
Calculate Phenotype Risk Scores
.Rbuildignore
.github/workflows/check-deploy.yaml
.github/workflows/lint.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
CRAN-SUBMISSION
DESCRIPTION
NAMESPACE
NEWS.md
R/examples.R
R/genetic_association.R
R/genetic_diagnosis.R
R/map.R
R/phers.R
R/utils.R
R/weights.R
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/HPO_phecode_map.csv.gz
data-raw/ICD_phecode_map.csv.gz
data-raw/all_demos_sd.sql
data-raw/all_icds_sd.sql
data-raw/disease_dx_icd_map_omim.csv.gz
data-raw/disease_hpo_map_omim.csv.gz
data-raw/phers_create_data.R
data-raw/pre_calculated_weights.csv.gz
data/HPOPhecodeMap.rda
data/ICDPhecodeMap.rda
data/demoSample.rda
data/diseaseDxIcdMap.rda
data/diseaseHPOMap.rda
data/icdSample.rda
data/preCalcWeights.rda
inst/extdata/geno_sample-temporary.simfreq
inst/extdata/geno_sample.bed
inst/extdata/geno_sample.bim
inst/extdata/geno_sample.fam
inst/extdata/geno_sample.log
inst/extdata/run_plink.R
inst/extdata/wgas.sim
lint_ignore.csv
man/demoSample.Rd
man/diseaseDxIcdMap.Rd
man/diseaseHpoMap.Rd
man/getDxStatus.Rd
man/getGeneticAssociations.Rd
man/getPhecodeOccurrences.Rd
man/getResidualScores.Rd
man/getScores.Rd
man/getWeights.Rd
man/hpoPhecodeMap.Rd
man/icdPhecodeMap.Rd
man/icdSample.Rd
man/mapDiseaseToPhecode.Rd
man/preCalcWeights.Rd
phers.Rproj
tests/testthat.R
tests/testthat/data/geno_test.bed
tests/testthat/data/geno_test.bim
tests/testthat/data/geno_test.fam
tests/testthat/data/get_genetic_associations_additive_output.qs
tests/testthat/data/get_residual_scores_output.qs
tests/testthat/data/get_weights_cox_negative_output.qs
tests/testthat/data/get_weights_cox_output.qs
tests/testthat/data/get_weights_logistic_negative_output.qs
tests/testthat/data/get_weights_logistic_output.qs
tests/testthat/data/get_weights_loglinear_output.qs
tests/testthat/data/get_weights_prevalence_negative_output.qs
tests/testthat/data/get_weights_prevalence_output.qs
tests/testthat/data/get_weights_prevalence_precalc_output.qs
tests/testthat/data/run_linear_additive_output.qs
tests/testthat/data/run_linear_dominant_output.qs
tests/testthat/data/run_linear_genotypic_output.qs
tests/testthat/data/run_linear_recessive_output.qs
tests/testthat/setup.R
tests/testthat/test_genetic_association.R
tests/testthat/test_genetic_diagnosis.R
tests/testthat/test_map.R
tests/testthat/test_phers.R
tests/testthat/test_weights.R
