GWAS summary statistics | Reference data | Harmonize GWAS summary to the reference data | Map SNPs to genes | Perform gene-based association tests
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.zip(r-4.7-x86_64)snpsettest_0.1.2.zip(r-4.7-arm64)snpsettest_0.1.2.zip(r-4.6-x86_64)snpsettest_0.1.2.zip(r-4.6-arm64)snpsettest_0.1.2.zip(r-4.5-x86_64)
snpsettest_0.1.2.tgz(r-4.6-x86_64)snpsettest_0.1.2.tgz(r-4.6-arm64)snpsettest_0.1.2.tgz(r-4.5-x86_64)snpsettest_0.1.2.tgz(r-4.5-arm64)
snpsettest_0.1.2.tar.gz(r-4.7-arm64)snpsettest_0.1.2.tar.gz(r-4.7-x86_64)snpsettest_0.1.2.tar.gz(r-4.6-arm64)snpsettest_0.1.2.tar.gz(r-4.6-x86_64)
snpsettest_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
snpsettest/json (API)
| # Install 'snpsettest' in R: |
| install.packages('snpsettest', repos = c('https://himesgroup.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/himesgroup/snpsettest/issues
Uses libs:
Datasets:
- 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 from:38d5b86217. Checks:15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 109 | ||
| linux-devel-x86_64 | OK | 140 | ||
| source / vignettes | OK | 184 | ||
| linux-release-arm64 | OK | 131 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 219 | ||
| macos-release-x86_64 | OK | 268 | ||
| macos-oldrel-arm64 | OK | 192 | ||
| macos-oldrel-x86_64 | OK | 334 | ||
| windows-devel-arm64 | OK | 371 | ||
| windows-devel-x86_64 | OK | 160 | ||
| windows-release-arm64 | OK | 341 | ||
| windows-release-x86_64 | OK | 95 | ||
| windows-oldrel-x86_64 | OK | 109 | ||
| wasm-release | OK | 104 |
Exports:harmonize_sumstatsmap_snp_to_generead_reference_bedsnpset_test
Dependencies:data.tablegastonRcppRcppArmadilloRcppEigenRcppParallel
Introduction to snpsettest
Last update: 2023-09-09
Started: 2021-02-22
A set-based association test in snpsettest
Last update: 2023-09-09
Started: 2021-02-02
Processing 1000 Genomes data for set-based association tests
Overview | Prerequisites | Choose an appropriate population | Convert the 1000 Genomes data to PLINK 1 binary format | Read PLINK 1 binary fileset to R session
Last update: 2021-02-27
Started: 2021-02-02
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 |