diff --git a/DESCRIPTION b/DESCRIPTION index b6601db..f91cee2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,12 +6,14 @@ Authors@R: c( person('Paul', 'Boutros', role = 'cre', email = 'PBoutros@mednet.ucla.edu'), person('Nicole', 'Zeltser', role = 'aut', comment = c(ORCID = '0000-0001-7246-2771')), person('Rachel', 'Dang', role = 'ctb')) -Description: This tool is intended to simply and transparently parse - genotype/dosage data from an input VCF, match genotype coordinates - to the component SNPs of an existing polygenic score, and apply - SNP weights to dosages to calculate a polygenic score for each - individual in accordance with the additive weighted sum of dosages - model. +Description: Simple and transparent parsing of genotype/dosage data + from an input Variant Call Format (VCF) file, matching of genotype + coordinates to the component Single Nucleotide Polymorphisms (SNPs) + of an existing polygenic score (PGS), and application of SNP weights + to dosages for the calculation of a polygenic score for each individual + in accordance with the additive weighted sum of dosages model. Methods + are designed in reference to best practices described by + Collister, Liu, and Clifton (2022) . Depends: R (>= 4.2.0) Imports: diff --git a/R/apply-pgs.R b/R/apply-pgs.R index 2857701..bd33518 100644 --- a/R/apply-pgs.R +++ b/R/apply-pgs.R @@ -246,7 +246,7 @@ apply.polygenic.score <- function( validate.phenotype.data.input(phenotype.data = phenotype.data, phenotype.analysis.columns = phenotype.analysis.columns, vcf.data = vcf.data); if (validate.inputs.only) { - print('Input data passed validation\n'); + message('Input data passed validation'); return(TRUE); } diff --git a/tests/testthat/test-pgs-application.R b/tests/testthat/test-pgs-application.R index a83ef0f..c1431e7 100644 --- a/tests/testthat/test-pgs-application.R +++ b/tests/testthat/test-pgs-application.R @@ -210,6 +210,14 @@ test_that( ), TRUE ); + expect_message( + apply.polygenic.score( + vcf.data = simple.pgs.application.test.data$vcf.data, + pgs.weight.data = simple.pgs.application.test.data$pgs.weight.data, + validate.inputs.only = TRUE + ), + 'Input data passed validation' + ); } );