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-4.5)finemapr_0.1.0.zip(r-4.4)finemapr_0.1.0.zip(r-4.3)
finemapr_0.1.0.tgz(r-4.4-any)finemapr_0.1.0.tgz(r-4.3-any)
finemapr_0.1.0.tar.gz(r-4.5-noble)finemapr_0.1.0.tar.gz(r-4.4-noble)
finemapr_0.1.0.tgz(r-4.4-emscripten)finemapr_0.1.0.tgz(r-4.3-emscripten)
finemapr.pdf |finemapr.html✨
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 10 months agofrom:d99c5ac89d (on suggestions). Checks:ERROR: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 31 2024 |
| R-4.5-win | ERROR | Oct 31 2024 |
| R-4.5-linux | ERROR | Oct 31 2024 |
| R-4.4-win | ERROR | Oct 31 2024 |
| R-4.4-mac | ERROR | Oct 31 2024 |
| R-4.3-win | ERROR | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:abfcojocollect_resultsexample_finemapextract_credible_setfilename_annotfilename_configfilename_kfilename_ldfilename_logfilename_masterfilename_snpfilename_zscorefinemaprplot_configplot_ncausalplot_snpplot_zscoreprint.Finemaprprint.FinemaprCaviarprint.FinemaprFinemapprint.FinemaprPaintorprocess_annotprocess_ldprocess_nprocess_tabproxysnps_ref_ldproxysnps_ref_vcfread_ldread_zscoreref_bedref_ldref_poprun_caviarrun_cojorun_finemaprun_paintorrun_toolsumstats_bmiwrite_files
Dependencies:bitbit64clicliprcolorspacecowplotcpp11crayondata.tabledplyrfansifarvergenericsggplot2ggrepelgluegtablehmsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigprettyunitsprogressR6RColorBrewerRcppreadrrlangscalestibbletidyselecttzdbutf8vctrsviridisLitevroomwithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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. | 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 |