Package: genepi.utils 0.0.31

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_0.0.31.tar.gz
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genepi.utils_0.0.31.tgz(r-4.4-any)genepi.utils_0.0.31.tgz(r-4.3-any)
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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'))

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

On CRAN:

43 exports 7 stars 3.94 score 188 dependencies 10 scripts

Last updated 19 days agofrom:2d97072d80. Checks:ERROR: 1 WARNING: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	FAIL	Sep 17 2024
R-4.5-win	WARNING	Sep 17 2024
R-4.5-linux	WARNING	Sep 17 2024
R-4.4-win	WARNING	Sep 17 2024
R-4.4-mac	WARNING	Sep 17 2024
R-4.3-win	WARNING	Sep 17 2024
R-4.3-mac	WARNING	Sep 17 2024

Exports:as.data.table chrpos_to_rsid clump clump_mr collider_bias Column ColumnMap cwls dudbridge eaf_plot generate_random_gwas_data get_pfile_variants get_proxies GWAS harmonise ld_matrix lift manhattan miami MR mr_egger mr_ivw mr_pcgmm mr_results_to_data_table mr_weighted_median mr_weighted_mode plot_coloc_probabilities plot_mr qq_plot reset_index_snp run_mr set_1000G_reference set_dbsnp_directory set_ld_mat set_plink2 slopehunter subset_gwas to_MRInput to_MRMVInput which_1000G_reference which_dbsnp_builds which_dbsnp_directory which_plink2

Dependencies:abind arrangements askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops boot broom bslib cachem car carData cli clipr codetools colorspace CompQuadForm corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray DEoptimR Deriv digest doBy dplyr evaluate fansi farver fastmap fontawesome foreach formatR fs fst fstcore furrr futile.logger futile.options future generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glmnet globals glue gmp GPArotation gridExtra gtable highr hms htmltools htmlwidgets httr ieugwasr indexevent IRanges isoband iterators iterpc jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle listenv lme4 magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats mclust memoise MendelianRandomization meta metadat metafor mgcv microbenchmark mime minqa mnormt modelr mr.raps MRMix MRPRESSO munsell nlme nloptr nnet nortest numDeriv openssl parallelly pbapply pbkrtest pillar pkgconfig plotly plyr polynom prettyunits progress progressr promises psych purrr quantreg R6 RadialMR rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr reshape2 restfulr Rhtslib rjson rlang rmarkdown robustbase Rsamtools rstatix rtracklayer S4Arrays S4Vectors S7 sass scales shape SlopeHunter snow SparseArray SparseM stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TwoSampleMR tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

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Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
as.data.table	as.data.table
Chromosome & position data to variant RSID	chrpos_to_rsid
Clump a GWAS	clump
Clump MR object exposure	clump_mr
Run collider bias assessment	collider_bias
Column object	Column
ColumnMap object	ColumnMap
Corrected Weighted Least Squares collider bias method	cwls
Dudbridge collider bias method	dudbridge
Effect allele frequency plot	eaf_plot
Generate random GWAS data	generate_random_gwas_data
Extract variants from plink binary	get_pfile_variants
Get proxies for variants from plink binary	get_proxies
GWAS object	GWAS
Harmonise GWAS effects	harmonise
Calculate LD matrix	ld_matrix
Liftover GWAS positions	lift
Manhattan plot	manhattan
Miami plot	miami
MR object	MR
Run Egger MR	mr_egger
Run IVW MR	mr_ivw
Run PC-GMM MR	mr_pcgmm
MR results to data.table	mr_results_to_data_table
Run weighted median MR	mr_weighted_median
Run weighted mode MR	mr_weighted_mode
Coloc probability plot	plot_coloc_probabilities
Plot MR results	plot_mr
QQ plot	qq_plot
Reset index SNP	reset_index_snp
Run MR	run_mr
Set the 1000G reference path	set_1000G_reference
Set dbSNP directory	set_dbsnp_directory
Set the LD matrix	set_ld_mat
Set the PLINK2 path	set_plink2
Slope-Hunter collider bias method	slopehunter
subset_gwas	subset_gwas
Convert to MendelianRandomization::MRInput object	to_MRInput
Convert to MendelianRandomization::MRMVInput object	to_MRMVInput
Get 1000G reference path(s)	which_1000G_reference
Get available dbSNP builds	which_dbsnp_builds
Get dbSNP directory	which_dbsnp_directory
Get plink2 path	which_plink2