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项目作者： variani

项目描述 ：
Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF
高级语言： R
项目地址: git://github.com/variani/finemapr.git
创建时间： 2018-02-09T17:19:05Z
项目社区：https://github.com/variani/finemapr
开源协议：GNU General Public License v3.0
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finemapr

travis-ci build status

R interface to fine-mappers:

By using finemapr, your input files are automatically prepared for each tool, the analysis workflow is tool-independent; and exploration of fine-mapping results is powered by R in printing/plotting/data export.

Note: the package is still under development and its current version is not stable. The current work aims at switching from run_<tool> functions to a more general one, finemapr. The later function makes use of S3 method dispatch features. Thus, use this package with caution until the stable release comes out.

Quick start

  1. library(finemapr)
  2. library(tidyverse)
  4. # get some example data
  5. finemapr::example_finemap() %>% attach
  7. # run finemapping, default tool is finemap
  8. out <- finemapr(z1, ld1, n1, args = "--n-causal-max 3")
  10. # print & plot results
  11. out
  13. plot(out, grid_nrow = 1)

Tool-independent analysis workflow

  1. # set up
  2. options(finemapr_<tool> = "<path to fine-mapping tool>")
  4. # read input files
  5. my_zscores <- read_zscores("<my_scores.tab>")
  6. my_ld <- read_ld("<my_ld.tab>")
  8. # run analysis
  9. # depreciated, but still works: out <- run_<tool>(my_zscores, my_ld, args = "<custom arguments>")
  10. out <- finemapr(my_zscores, my_ld, method = "<tool>", args = "<custom arguments>")
  12. # explore results
  13. print(out)
  14. head(out$snp) # main table of results
  15. plot(out)
  17. # export results
  18. write.table(out$snp, "<my_results.tab>")

Examples

See the vignette Fine-mapping analysis pipeline by finemapr.