Package: CheckSumStats 0.0.0.9000
Philip Haycock
CheckSumStats: CheckSumStats
CheckSumStats is an R package for checking the accuracy of meta- and summary-data from genome-wide association studies (GWAS) prior to their use in post-GWAS applications. For example, the package provides tools for checking that the reported effect allele and effect allele frequency columns are correct. It also checks for possible issues in the reported effect sizes that might introduce bias into downstream analyses.
Authors:
CheckSumStats_0.0.0.9000.tar.gz
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CheckSumStats_0.0.0.9000.tgz(r-4.4-any)CheckSumStats_0.0.0.9000.tgz(r-4.3-any)
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CheckSumStats.pdf |CheckSumStats.html✨
CheckSumStats/json (API)
| # Install 'CheckSumStats' in R: |
| install.packages('CheckSumStats', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mrcieu/checksumstats/issues
- ara_test_dat - A example dataset of genetic summary data for arachidonic acid
- charge_top_hits - GWAS top hits for arachidonic acid in the CHARGE consortium
- charge_top_hits_cleaned - GWAS top hits for arachidonic acid in the CHARGE consortium after post-GWAS cleaning
- glioma_test_dat - A example dataset of genetic summary data
- refdat_1000G_superpops - A dataset of reference allele frequencies from 1000 genomes superpopulations
Last updated 1 years agofrom:ba670767d4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 01 2024 |
| R-4.5-win | NOTE | Oct 01 2024 |
| R-4.5-linux | NOTE | Oct 01 2024 |
| R-4.4-win | NOTE | Oct 01 2024 |
| R-4.4-mac | NOTE | Oct 01 2024 |
| R-4.3-win | NOTE | Oct 01 2024 |
| R-4.3-mac | NOTE | Oct 01 2024 |
Exports:combine_plotscompare_effect_to_gwascatalogcompare_effect_to_gwascatalog2extract_sig_snpsextract_snpsfind_hits_in_gwas_catalogflag_af_conflictsflag_gc_conflictsflag_gc_conflicts2format_dataget_efogwas_catalog_hitsinfer_ancestrymake_plot_gwas_catalogmake_plot_mafmake_plot_pred_effectmake_snplistpredict_beta_sdpredict_lnor_shtransform_betaszz_plot
Dependencies:abindAnnotationDbiaskpassassertthatbackportsBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbriobroomcachemcallrcarcarDataclicolorspaceconcatenatecorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdescdiffobjdigestdoBydplyrevaluatefansifarverfastmapfilelockFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegwasrapiddhighrhmshttrhttr2ieugwasrIRangesisobandjsonliteKEGGRESTknitrlabelinglatticelifecyclelme4lubridatemagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpingrpkgbuildpkgconfigpkgloadplogrplyrpngpolynompraiseprettyunitsprocessxprogresspspurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrematch2rlangrprojrootRSQLiterstatixS4VectorsscalesSparseMstringistringrsurvivalsystestthattibbletidyrtidyselecttimechangetriebeardUCSC.utilsurltoolsutf8vctrsviridisLitewaldowithrwritexlxfunxml2XVectoryamlzlibbioc
