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:Philip Haycock [aut, cre]

CheckSumStats_0.0.0.9000.tar.gz
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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

Datasets:

On CRAN:

Conda:

3.00 score 8 stars 25 scripts 21 exports 140 dependencies

Last updated 2 years agofrom:ba670767d4. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 19 2025
R-4.5-winNOTEMar 19 2025
R-4.5-macNOTEMar 19 2025
R-4.5-linuxNOTEMar 19 2025
R-4.4-winNOTEMar 19 2025
R-4.4-macNOTEMar 19 2025
R-4.4-linuxNOTEMar 19 2025
R-4.3-winNOTEMar 19 2025
R-4.3-macNOTEMar 19 2025

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:abindAnnotationDbiaskpassassertthatbackportsBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobbootbriobroomcachemcallrcarcarDataclicolorspaceconcatenatecorrplotcowplotcpp11crayoncurlDBIdbplyrDerivdescdiffobjdigestdoBydplyrevaluatefansifarverfastmapfilelockFormulafsgenericsGenomeInfoDbGenomeInfoDbDataggplot2ggpubrggrepelggsciggsignifgluegridExtragtablegwasrapiddhighrhmshttrhttr2ieugwasrIRangesisobandjsonliteKEGGRESTknitrlabelinglatticelifecyclelme4lubridatemagrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpingrpkgbuildpkgconfigpkgloadplogrplyrpngpolynompraiseprettyunitsprocessxprogresspspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangrprojrootRSQLiterstatixS4VectorsscalesSparseMstringistringrsurvivalsystestthattibbletidyrtidyselecttimechangetriebeardUCSC.utilsurltoolsutf8vctrsviridisLitewaldowithrwritexlxfunxml2XVectoryaml