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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-4.7)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✨
DESCRIPTION
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

On CRAN:

3.00 score 6 scripts 36 exports 41 dependencies

Last updated from:ccbd6f4dd8 (on suggestions-2). Checks:7 WARNING, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	WARNING	173
source / vignettes	OK	241
linux-release-x86_64	WARNING	162
macos-release-arm64	WARNING	89
macos-oldrel-arm64	WARNING	92
windows-devel	WARNING	108
windows-release	WARNING	133
windows-oldrel	WARNING	110
wasm-release	OK	125

Exports:abf cojo collect_results example_finemap extract_credible_set filename_annot filename_config filename_k filename_ld filename_log filename_master filename_snp filename_zscore finemapr plot_config plot_ncausal plot_snp plot_zscore process_annot process_ld process_n process_tab proxysnps_ref_ld proxysnps_ref_vcf read_ld read_zscore ref_bed ref_ld ref_pop run_caviar run_cojo run_finemap run_paintor run_tool sumstats_bmi write_files

Dependencies:bit bit64 cli clipr cowplot cpp11 crayon data.table dplyr farver generics ggplot2 ggrepel glue gtable hms isoband labeling lattice lifecycle magrittr Matrix pillar pkgconfig prettyunits progress R6 RColorBrewer Rcpp readr rlang S7 scales tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr

Fine-mapping analysis pipeline by finemapr

Rendered fromfinemapr.Rmdusingknitr::rmarkdown

Last update: 2025-08-01
Started: 2018-02-19

Citation

Development and contributors

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