Package: finemapr 0.1.0

Andrey Ziyatdinov

finemapr: R wrapper to fine-mappers

R wrapper to fine-mappers.

Authors:Andrey Ziyatdinov [aut, cre]

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'))

Peer review:

Bug tracker:https://github.com/variani/finemapr/issues

On CRAN:

1.70 score 6 scripts 40 exports 46 dependencies

Last updated 11 months agofrom:d99c5ac89d (on suggestions). Checks:ERROR: 7. Indexed: no.

TargetResultDate
Doc / VignettesFAILNov 27 2024
R-4.5-winERRORNov 27 2024
R-4.5-linuxERRORNov 27 2024
R-4.4-winERRORNov 27 2024
R-4.4-macERRORNov 27 2024
R-4.3-winERRORNov 27 2024
R-4.3-macERRORNov 27 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 pageTopics
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.Rproxysnps_ref_ld
https://github.com/slowkow/proxysnps/blob/master/R/get_vcf.Rproxysnps_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-Heritabilitysumstats_bmi