remlapmot. To fix this you can add URL: https://mrcieu.r-universe.dev/finemapr to the package DESCRIPTION file. See also theR-universe documentation.Package: finemapr 0.1.0
Andrey Ziyatdinov
finemapr: R wrapper to fine-mappers
R wrapper to fine-mappers.
Authors:
finemapr_0.1.0.tar.gz
finemapr_0.1.0.zip(r-4.7)finemapr_0.1.0.zip(r-4.6)finemapr_0.1.0.zip(r-4.5)
finemapr_0.1.0.tgz(r-4.6-any)finemapr_0.1.0.tgz(r-4.5-any)
finemapr_0.1.0.tar.gz(r-4.7-any)finemapr_0.1.0.tar.gz(r-4.6-any)
finemapr_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
finemapr/json (API)
| # Install 'finemapr' in R: |
| install.packages('finemapr', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/variani/finemapr/issues
Last updated from:ccbd6f4dd8 (on suggestions-2). Checks:7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 178 | ||
| source / vignettes | OK | 235 | ||
| linux-release-x86_64 | WARNING | 169 | ||
| macos-release-arm64 | WARNING | 99 | ||
| macos-oldrel-arm64 | WARNING | 125 | ||
| windows-devel | WARNING | 130 | ||
| windows-release | WARNING | 154 | ||
| windows-oldrel | WARNING | 118 | ||
| wasm-release | OK | 122 |
Exports:abfcojocollect_resultsexample_finemapextract_credible_setfilename_annotfilename_configfilename_kfilename_ldfilename_logfilename_masterfilename_snpfilename_zscorefinemaprplot_configplot_ncausalplot_snpplot_zscoreprocess_annotprocess_ldprocess_nprocess_tabproxysnps_ref_ldproxysnps_ref_vcfread_ldread_zscoreref_bedref_ldref_poprun_caviarrun_cojorun_finemaprun_paintorrun_toolsumstats_bmiwrite_files
Dependencies:bitbit64clicliprcowplotcpp11crayondata.tabledplyrfarvergenericsggplot2ggrepelgluegtablehmsisobandlabelinglatticelifecyclemagrittrMatrixpillarpkgconfigprettyunitsprogressR6RColorBrewerRcppreadrrlangS7scalestibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| abf | abf |
| Run GCTA-COJO. | cojo |
| S3 class FinemaprFinemap. | collect_results.FinemaprFinemap filename_config.FinemaprFinemap filename_k.FinemaprFinemap filename_ld.FinemaprFinemap filename_log.FinemaprFinemap filename_master.FinemaprFinemap filename_snp.FinemaprFinemap filename_zscore.FinemaprFinemap FinemaprFinemap plot.FinemaprFinemap plot_config.FinemaprFinemap plot_ncausal.FinemaprFinemap plot_snp.FinemaprFinemap print.FinemaprFinemap run_tool.FinemaprFinemap write_files.FinemaprFinemap |
| S3 class FinemaprPaintor. | collect_results.FinemaprPaintor filename_annot.FinemaprPaintor filename_ld.FinemaprPaintor filename_master.FinemaprPaintor filename_snp.FinemaprPaintor filename_zscore.FinemaprPaintor FinemaprPaintor print.FinemaprPaintor process_annot.FinemaprPaintor run_tool.FinemaprPaintor write_files.FinemaprPaintor |
| Run FINEMAP. | finemapr |
| S3 class FinemaprCaviar. | FinemaprCaviar plot.FinemaprCaviar plot_snp.FinemaprCaviar print.FinemaprCaviar |
| Package finemapr. | finemapr-package finemaprPackage |
| S3 class Finemapr. | extract_credible_set.Finemapr Finemapr plot.Finemapr plot_ncausal plot_snp.Finemapr plot_zscore.Finemapr print.Finemapr process_ld.Finemapr process_tab.Finemapr |
| https://github.com/slowkow/proxysnps/blob/master/R/get_vcf.R | proxysnps_ref_ld |
| https://github.com/slowkow/proxysnps/blob/master/R/get_vcf.R | proxysnps_ref_vcf |
| Read LD matrix from a file. | read_ld |
| Read z-scores from a file. | read_zscore |
| Run CAVIAR. | run_caviar |
| Run FINEMAP. | run_finemap |
| Run Paintor. | run_paintor |
| https://data.broadinstitute.org/alkesgroup/sumstats_formatted/readme.txt https://github.com/bulik/ldsc/wiki/Partitioned-Heritability | sumstats_bmi |