biona001 / ghostknockoffgwas Goto Github PK

View Code? Open in Web Editor NEW

5.0 1.0 1.0 11.67 MB

Package for analyzing GWAS summary statistics data

License: MIT License

Julia 84.15% R 15.85%

conditional-independence false-discovery-rate fdr genomics gwas knockoffs summary-statistics variable-selection

ghostknockoffgwas's Issues

Roadmap until 1.0 release

Features to add:

Add knockoff q-values to output (see eq19 of this paper)
Ability to read different columns in zfile, based on user input
Add code to make manhattan plot and show this in documentation
Within-group knockoff filter (see this paper)

Rather than compiling binaries for GhostKnockoffGWAS via PackageCompiler.jl, consider providing a docker image, see this example. Dockers provide an alternative way to run GhostKnockoffGWAS, even on non-linux machines without Julia installed

manhattan plots not utilizing within-group knockoff filter

Error in CMplot

As reported by @GuJQ5, an error appears when drawing the manhattan plot:

Error in CMplot(x1t, plot.type = "m", LOG10 = FALSE, col = c("grey30",  :

  unused argument (bin.range = c(0, 500))

The reason is that the CMplot package has been update on Jan 19, 2024, where the argument bin.range is removed in the latest version.

wget `example_zfile.txt` broken

2 things to fix in the quick start of documentation

In step (1), the download link to the software is fixed at v0.1.0. It should be the latest version
The 3rd step actually doesn't work.

Improve documentation

Readme should describe GhostKnockoffGWAS in relation to mainstream GWAS methods, as most users won't be familiar with knockoff based inference.
The developer documentation is a little obsolete and should be revamped. In particular, the syntax for calling BlockGroupGhostMatrix (which depended on R package ghostbasil) should be updated to the syntax used by Ghostbasil.jl.
Gallery: We should include a few manhattan plots comparing marginal vs knockoff analysis

very slow manhattan plots

It seems like when there are a lot of discoveries (e.g. > 100), it takes a really long time (>20h) to generate the resulting manhattan plots

FileIO error

As reported by @GuJQ5, there is some problem with reading .h5 formatted LD files.

$ app_linux_x86/bin/GhostKnockoffGWAS --zfile UCB_GWAS.txt.gz --LD-files EUR --N 44161 --genome-build 19 --out UCB_GWAS_results

┌ Warning: Error requiring `UnPack` from `JLD2`
│ exception = 
│ IOError: stat("/home/groups/sabatti/.julia/packages/JLD2/ryhNR/ext/UnPackExt.jl"): permission denied (EACCES) 
│ Stacktrace: 
│ [1] uv_error 
│ @ ./libuv.jl:100 [inlined] 
│ [2] stat(path::String) 
│ @ Base.Filesystem ./stat.jl:152 
│ [3] isfile(path::String) 
│ @ Base.Filesystem ./stat.jl:461 
│ [4] macro expansion 
│ @ /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/Requires.jl:37 [inlined] 
│ [5] top-level scope 
│ @ /home/groups/sabatti/.julia/packages/JLD2/ryhNR/src/JLD2.jl:607 
│ [6] eval 
│ @ ./boot.jl:370 [inlined] 
│ [7] eval 
│ @ /home/groups/sabatti/.julia/packages/JLD2/ryhNR/src/JLD2.jl:1 [inlined] 
 [8] (::JLD2.var"#131#134")() 
│ @ JLD2 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:101 
│ [9] macro expansion 
│ @ ./timing.jl:393 [inlined] 
│ [10] err(f::Any, listener::Module, modname::String, file::String, line::Any) 
│ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:47 
│ [11] (::JLD2.var"#130#133")() 
│ @ JLD2 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:100 
│ [12] withpath(f::Any, path::String) 
│ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:37 
│ [13] (::JLD2.var"#129#132")() 
│ @ JLD2 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:99 
│ [14] listenpkg(f::Any, pkg::Base.PkgId) 
│ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:20 
│ [15] macro expansion 
│ @ /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:98 [inlined] 
│ [16] __init__() 
│ @ JLD2 /home/groups/sabatti/.julia/packages/JLD2/ryhNR/src/JLD2.jl:606 
└ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:51 

┌ Warning: Error requiring `FileIO` from `HDF5` 
│ exception = 
│ IOError: stat("/home/groups/sabatti/.julia/packages/HDF5/HtnQZ/src/fileio.jl"): permission denied (EACCES) 
│ Stacktrace: 
│ [1] uv_error 
│ @ ./libuv.jl:100 [inlined] 
│ [2] stat(path::String) 
│ @ Base.Filesystem ./stat.jl:152 
│ [3] isfile(path::String) 
│ @ Base.Filesystem ./stat.jl:461 
│ [4] top-level scope 
│ @ /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/Requires.jl:37 
│ [5] eval 
│ @ ./boot.jl:370 [inlined] 
│ [6] eval 
│ @ /home/groups/sabatti/.julia/packages/HDF5/HtnQZ/src/HDF5.jl:1 [inlined] 
│ [7] (::HDF5.var"#115#121")() 
│ @ HDF5 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:101 
│ [8] macro expansion 
│ @ ./timing.jl:393 [inlined] 
│ [9] err(f::Any, listener::Module, modname::String, file::String, line::Any) 
│ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:47 
│ [10] (::HDF5.var"#114#120")() 
│ @ HDF5 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:100 
│ [11] withpath(f::Any, path::String) 
│ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:37 
│ [12] (::HDF5.var"#113#119")() 
│ @ HDF5 /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:99 
│ [13] listenpkg 
│ @ /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:20 [inlined] 
│ [14] macro expansion 
│ @ /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:98 [inlined] 
│ [15] __init__() 
│ @ HDF5 /home/groups/sabatti/.julia/packages/HDF5/HtnQZ/src/HDF5.jl:119 
└ @ Requires /home/groups/sabatti/.julia/packages/Requires/Z8rfN/src/require.jl:51 

Welcome to GhostKnockoffGWAS analysis! 
You have specified the following options: 
zfile = /oak/stanford/groups/zihuai/UCB data/Mar_13_James/UCB_GWAS.txt.gz 
LD_files = /oak/stanford/groups/zihuai/UCB data/Mar_13_James/EUR 
N (sample size) = 44161 
hg_build = 19 
outdir = /oak/stanford/groups/zihuai/UCB data/Mar_13_James/ 
outfile = /oak/stanford/groups/zihuai/UCB data/Mar_13_James/UCB_GWAS_results seed = 2023 
verbose = true 
random_shuffle = true 
skip_shrinkage_check = false 

count_matchable_snps processed chr 1, cumulative SNPs = 46145 
count_matchable_snps processed chr 2, cumulative SNPs = 94450 
count_matchable_snps processed chr 3, cumulative SNPs = 135010 
count_matchable_snps processed chr 4, cumulative SNPs = 173294 
count_matchable_snps processed chr 5, cumulative SNPs = 209902 
count_matchable_snps processed chr 6, cumulative SNPs = 253171 
count_matchable_snps processed chr 7, cumulative SNPs = 285925 
count_matchable_snps processed chr 8, cumulative SNPs = 316982 
count_matchable_snps processed chr 9, cumulative SNPs = 343328 
count_matchable_snps processed chr 10, cumulative SNPs = 373313 
count_matchable_snps processed chr 11, cumulative SNPs = 403207 
count_matchable_snps processed chr 12, cumulative SNPs = 431788 
count_matchable_snps processed chr 13, cumulative SNPs = 452614 
count_matchable_snps processed chr 14, cumulative SNPs = 471730 
count_matchable_snps processed chr 15, cumulative SNPs = 489924 
count_matchable_snps processed chr 16, cumulative SNPs = 510232 
count_matchable_snps processed chr 17, cumulative SNPs = 528617 
count_matchable_snps processed chr 18, cumulative SNPs = 546334 
count_matchable_snps processed chr 19, cumulative SNPs = 561544 
count_matchable_snps processed chr 20, cumulative SNPs = 576703 
count_matchable_snps processed chr 21, cumulative SNPs = 585317 
count_matchable_snps processed chr 22, cumulative SNPs = 594385 
Error encountered while load FileIO.File{FileIO.DataFormat{:HDF5}, String}("EUR/chr1/LD_start100826405_end102041015.h5"). 

Fatal error: 
ERROR: HDF5 load error: neither load nor fileio_load is defined 
due to FileIO.SpecError(HDF5, :load) 
Will try next loader. 

Stacktrace: 
[1] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:209 
[2] action 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined] 
[3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 
[4] action 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined] 
[5] load(::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113 
[6] load 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109 [inlined] 
[7] macro expansion 
@ /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/ghostbasil_parallel.jl:131 [inlined] 
[8] macro expansion 
@ ./timing.jl:393 [inlined] 
[9] ghostknockoffgwas(LD_files::String, z::Vector{Float64}, chr::Vector{Int64}, pos::Vector{Int64}, effect_allele::Vector{String}, non_effect_allele::Vector{String}, N::Int64, hg_build::Int64, outdir::String; outname::String, seed::Int64, target_chrs::Vector{Int64}, A_scaling_factor::Float64, kappa_lasso::Float64, LD_shrinkage::Bool, target_fdrs::Vector{Float64}, verbose::Bool, skip_shrinkage_check::Bool, random_shuffle::Bool) 
@ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/ghostbasil_parallel.jl:130 
[10] macro expansion 
@ /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/app.jl:43 [inlined] 
[11] macro expansion 
@ ./timing.jl:393 [inlined] 
[12] julia_main() 
@ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/app.jl:42 
[13] top-level scope 
@ none:1

Stacktrace: 
[1] handle_error(e::FileIO.LoaderError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:61 
[2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/error_handling.jl:56
[3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:228 
[4] action 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:196 [inlined] 
[5] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 
[6] action 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:185 [inlined] 
[7] load(::String; options::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) 
@ FileIO /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:113 
[8] load 
@ /home/groups/sabatti/.julia/packages/FileIO/BE7iZ/src/loadsave.jl:109 [inlined] 
[9] macro expansion 
@ /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/ghostbasil_parallel.jl:131 [inlined] 
[10] macro expansion 
@ ./timing.jl:393 [inlined] 
[11] ghostknockoffgwas(LD_files::String, z::Vector{Float64}, chr::Vector{Int64}, pos::Vector{Int64}, effect_allele::Vector{String}, non_effect_allele::Vector{String}, N::Int64, hg_build::Int64, outdir::String; outname::String, seed::Int64, target_chrs::Vector{Int64}, A_scaling_factor::Float64, kappa_lasso::Float64, LD_shrinkage::Bool, target_fdrs::Vector{Float64}, verbose::Bool, skip_shrinkage_check::Bool, random_shuffle::Bool) 
@ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/ghostbasil_parallel.jl:130 
[12] macro expansion 
@ /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/app.jl:43 [inlined] 
[13] macro expansion 
@ ./timing.jl:393 [inlined] 
[14] julia_main() 
@ GhostKnockoffGWAS /home/groups/sabatti/.julia/dev/GhostKnockoffGWAS/src/app.jl:42 
[15] top-level scope 
@ none:1

Recommend Projects

React

A declarative, efficient, and flexible JavaScript library for building user interfaces.
Vue.js

🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
Typescript

TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
TensorFlow

An Open Source Machine Learning Framework for Everyone
Django

The Web framework for perfectionists with deadlines.
Laravel

A PHP framework for web artisans
D3

Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

javascript

JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
web

Some thing interesting about web. New door for the world.
server

A server is a program made to process requests and deliver data to clients.
Machine learning

Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Visualization

Some thing interesting about visualization, use data art
Game

Some thing interesting about game, make everyone happy.

Recommend Org

Facebook

We are working to build community through open source technology. NB: members must have two-factor auth.
Microsoft

Open source projects and samples from Microsoft.
Google

Google ❤️ Open Source for everyone.
Alibaba

Alibaba Open Source for everyone
D3

Data-Driven Documents codes.
Tencent

China tencent open source team.