Package: snpsettest 0.1.2
Jaehyun Joo
snpsettest: A Set-Based Association Test using GWAS Summary Statistics
The goal of 'snpsettest' is to provide simple tools that perform set-based association tests (e.g., gene-based association tests) using GWAS (genome-wide association study) summary statistics. A set-based association test in this package is based on the statistical model described in VEGAS (versatile gene-based association study), which combines the effects of a set of SNPs accounting for linkage disequilibrium between markers. This package uses a different approach from the original VEGAS implementation to compute set-level p values more efficiently, as described in <https://github.com/HimesGroup/snpsettest/wiki/Statistical-test-in-snpsettest>.
Authors:
snpsettest_0.1.2.tar.gz
snpsettest_0.1.2.tar.gz(r-4.5-noble)snpsettest_0.1.2.tar.gz(r-4.4-noble)
snpsettest_0.1.2.tgz(r-4.4-emscripten)snpsettest_0.1.2.tgz(r-4.3-emscripten)
snpsettest.pdf |snpsettest.html✨
snpsettest/json (API)
NEWS
| # Install 'snpsettest' in R: |
| install.packages('snpsettest', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/himesgroup/snpsettest/issues
- exGWAS - An example file of GWAS summary statistics
- gene.curated.GRCh37 - Human gene information from the GENCODE GRCh37 version
- gene.curated.GRCh38 - Human gene information from the GENCODE GRCh38 version
Last updated 1 years agofrom:53a05acdaf. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 04 2024 |
| R-4.5-linux-x86_64 | OK | Dec 04 2024 |
Exports:harmonize_sumstatsmap_snp_to_generead_reference_bedsnpset_test
Dependencies:data.tablegastonRcppRcppArmadilloRcppEigenRcppParallel
A set-based association test in snpsettest
Rendered fromsnpsettest_model.Rmdusingknitr::rmarkdownon Dec 04 2024.Last update: 2023-09-09
Started: 2021-03-16
Introduction to snpsettest
Rendered fromsnpsettest_intro.Rmdusingknitr::rmarkdownon Dec 04 2024.Last update: 2023-09-09
Started: 2021-03-16
Processing 1000 Genomes data for set-based association tests
Rendered fromreference_1000Genomes.Rmdusingknitr::rmarkdownon Dec 04 2024.Last update: 2021-03-16
Started: 2021-03-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| An example file of GWAS summary statistics | exGWAS |
| Human gene information from the GENCODE GRCh37 version | gene.curated.GRCh37 |
| Human gene information from the GENCODE GRCh38 version | gene.curated.GRCh38 |
| Harmonizing GWAS summary to reference data | harmonize_sumstats |
| Map SNPs to genes | map_snp_to_gene |
| Read a PLINK bed file for reference data | read_reference_bed |
| Set-based association tests | snpset_test |
