Files in ApplyPolygenicScore
Utilities for the Application of a Polygenic Score to a VCF
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
R/write-output-files.R
R/calculate-dosage.R
R/handle-multiallelic-sites.R
R/run-pgs-statistics.R
R/convert-pgs-to-bed.R
R/handle-weight-files.R
R/assess-strand-flip.R
R/combine-vcf-with-pgs.R
R/plot-pgs-rank.R
R/format-chromosome-utility.R
R/handle-vcf.R
R/variant-by-sample-matrix-utility.R
R/plot-pgs.R
R/apply-pgs.R
R/data/data.R
inst/doc/UserGuide.Rmd
inst/doc/UserGuide.R
inst/doc/UserGuide.html
inst/extdata/PGS003378_hmPOS_GRCh38.txt.gz
inst/extdata/phenotype.test.data.Rda
inst/extdata/HG001_GIAB.vcf.gz
inst/extdata/PGS000662_hmPOS_GRCh38.txt.gz
build/vignette.rds
tests/testthat.R
tests/testthat/test-output-file-writing.R
tests/testthat/test-bed-merge.R
tests/testthat/test-plotting.R
tests/testthat/test-vcf-import.R
tests/testthat/test-vcf-pgs-merge.R
tests/testthat/test-pgs-import.R
tests/testthat/test-pgs-statistics.R
tests/testthat/test-sample-by-snp-matrix-utility.R
tests/testthat/test-dosage-calculator.R
tests/testthat/test-pgs-application.R
tests/testthat/test-pgs-to-bed-conversion.R
tests/testthat/test-format-chrom-utility.R
tests/testthat/generate-test-data.R
tests/testthat/test-strand-flip-handling.R
tests/testthat/data/strand.flip.test.data.Rda
tests/testthat/data/tiny.pgs.test.data.Rda
tests/testthat/data/HG001_multiallelic-merged_GIAB.vcf.gz
tests/testthat/data/PGS003378_hmPOS_GRCh38_multiallelic-variants.txt
tests/testthat/data/tiny.bed.test.data.Rda
tests/testthat/data/PGS003766_hmPOS_GRCh38.txt.gz
tests/testthat/data/PGS003378_hmPOS_GRCh38_slop10.bed
tests/testthat/data/phenotype.test.data.Rda
tests/testthat/data/split.multiallelic.site.test.data.Rda
tests/testthat/data/PGS003378_hmPOS_GRCh38_weight-foo.txt
tests/testthat/data/PGS003378_hmPOS_GRCh38_weight-NR.txt
tests/testthat/data/HG001_GIAB.vcf.gz
tests/testthat/data/missing.genotype.test.data.Rda
tests/testthat/data/PGS003378_hmPOS_GRCh38_weight-OR.txt
tests/testthat/data/merged.multiallelic.site.test.data.Rda
tests/testthat/data/PGS003378_hmPOS_GRCh38.txt
tests/testthat/data/simple.pgs.application.test.data.Rda
tests/testthat/data/PGS003378_hmPOS_GRCh38_duplicated-variants.txt
tests/testthat/data/HG001_single-sample_GIAB.vcf.gz
tests/testthat/data/import.test.data.Rda
tests/testthat/data/sample.data.rda
tests/testthat/data/PGS000662_hmPOS_GRCh38.txt.gz
tests/testthat/data/HG001_multiallelic-split_GIAB.vcf.gz
tests/testthat/data/PGS000662_hmPOS_GRCh38.txt
vignettes/UserGuide.Rmd
vignettes/img/2024-07-18_vignette-example-correlation_pgs-scatter.png
vignettes/img/2024-07-18_vignette-example-phenotype_pgs-density.png
vignettes/img/2024-07-19_vignette-example-basic_pgs-rank-plot.png
vignettes/img/2024-07-18_vignette-example-basic_pgs-density.png
vignettes/img/2024-07-19_vignette-example-phenotype_pgs-rank-plot.png
man/convert.pgs.to.bed.Rd
man/assess.pgs.vcf.allele.match.Rd
man/check.pgs.weight.columns.Rd
man/run.pgs.regression.Rd
man/convert.alleles.to.pgs.dosage.Rd
man/get.pgs.percentiles.Rd
man/combine.pgs.bed.Rd
man/write.apply.polygenic.score.output.to.file.Rd
man/convert.allele.frequency.to.dosage.Rd
man/combine.vcf.with.pgs.Rd
man/format.chromosome.notation.Rd
man/import.vcf.Rd
man/create.pgs.rank.plot.Rd
man/create.pgs.density.plot.Rd
man/flip.DNA.allele.Rd
man/create.pgs.with.continuous.phenotype.plot.Rd
man/apply.polygenic.score.Rd
man/import.pgs.weight.file.Rd
man/parse.pgs.input.header.Rd
