Package: genepi.utils 0.0.33

Nicholas Sunderland

genepi.utils: GenEpi Utility Functions

The genepi.utils package is a collection of utility functions for working with genetic epidemiology data.

Authors:Nicholas Sunderland [aut, cre]

genepi.utils_0.0.33.tar.gz
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genepi.utils.pdf |genepi.utils.html✨
genepi.utils/json (API)

# Install 'genepi.utils' in R:
install.packages('genepi.utils', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nicksunderland/genepi.utils/issues

Pkgdown site:https://nicksunderland.github.io

On CRAN:

5.78 score 9 stars 8 scripts 43 exports 189 dependencies

Last updated 3 months agofrom:01a9483728. Checks:1 OK, 6 WARNING. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKDec 24 2024
R-4.5-winWARNINGDec 24 2024
R-4.5-linuxWARNINGDec 24 2024
R-4.4-winWARNINGDec 24 2024
R-4.4-macWARNINGDec 24 2024
R-4.3-winWARNINGDec 24 2024
R-4.3-macWARNINGOct 26 2024

Exports:as.data.tablechrpos_to_rsidclumpclump_mrcollider_biasColumnColumnMapcwlsdudbridgeeaf_plotgenerate_random_gwas_dataget_pfile_variantsget_proxiesGWASharmonise_gwasld_matrixliftmanhattanmiamiMRmr_eggermr_ivwmr_pcgmmmr_results_to_data_tablemr_weighted_medianmr_weighted_modeplot_coloc_probabilitiesplot_mrqq_plotreset_index_snprun_mrset_1000G_referenceset_dbsnp_directoryset_ld_matset_plink2slopehuntersubset_gwasto_MRInputto_MRMVInputwhich_1000G_referencewhich_dbsnp_buildswhich_dbsnp_directorywhich_plink2

Dependencies:abindarrangementsaskpassbackportsbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsbootbroombslibcachemcarcarDataclicliprcodetoolscolorspaceCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArrayDEoptimRDerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomeforeachformatRFormulafsfstfstcorefurrrfutile.loggerfutile.optionsfuturegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2ggpubrggrepelggsciggsignifglmnetglobalsgluegmpGPArotationgridExtragtablehighrhmshtmltoolshtmlwidgetshttrieugwasrindexeventIRangesisobanditeratorsiterpcjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelistenvlme4magrittrMASSmathjaxrMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoiseMendelianRandomizationmetametadatmetaformgcvmicrobenchmarkmimeminqamnormtmodelrmr.rapsMRMixMRPRESSOmunsellnlmenloptrnnetnortestnumDerivopensslparallellypbapplypbkrtestpillarpkgconfigplotlyplyrpolynomprettyunitsprogressprogressrpromisespsychpurrrquantregR6RadialMRrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownrobustbaseRsamtoolsrstatixrtracklayerS4ArraysS4VectorsS7sassscalesshapeSlopeHuntersnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytexTwoSampleMRtzdbUCSC.utilsutf8vctrsviridisviridisLitevroomwithrxfunXMLxml2XVectoryamlzlibbioc

CHR:POS to RSID mapping

Rendered fromchrpos_to_rsid.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-03-27
Started: 2023-11-04

Clumping

Rendered fromclumping.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-03-30
Started: 2023-11-15

Collider bias

Rendered fromcollider_bias.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-03-29
Started: 2023-11-13

LD matrix

Rendered fromld_matrix.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-03-27
Started: 2023-11-28

Plotting

Rendered fromplotting.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-10-24
Started: 2023-11-08

Rationale and key points

Rendered fromrationale.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-10-24
Started: 2024-07-24

Standardise GWAS

Rendered fromstandardise_gwas.Rmdusingknitr::rmarkdownon Dec 24 2024.

Last update: 2024-03-27
Started: 2023-11-04