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Package: SlopeHunter 1.1.0

Osama Mahmoud

SlopeHunter: Slope-Hunter: A ROBUST METHOD FOR COLLIDER BIAS CORRECTION IN CONDITIONAL GENOME-WIDE ASSOCIATION STUDIES

Studying genetic associations with prognosis (e.g. survival, disability, subsequent disease events) is problematic due to selection bias - also termed index event bias or collider bias - whereby selection on disease status can induce associations between causes of incidence with prognosis. The Slope-Hunter approach adjusts genetic associations for this bias assuming that the contribution of the set of genetic variants affecting incidence only to the heritability of incidence is at least as large as the contribution of those affecting both incidence and prognosis.

Authors:Osama Mahmoud [aut, cre, cph]

SlopeHunter_1.1.0.tar.gz
SlopeHunter_1.1.0.zip(r-4.7)SlopeHunter_1.1.0.zip(r-4.6)SlopeHunter_1.1.0.zip(r-4.5)
SlopeHunter_1.1.0.tgz(r-4.6-any)SlopeHunter_1.1.0.tgz(r-4.5-any)
SlopeHunter_1.1.0.tar.gz(r-4.7-any)SlopeHunter_1.1.0.tar.gz(r-4.6-any)
SlopeHunter_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SlopeHunter/json (API)

# Install 'SlopeHunter' in R:

install.packages('SlopeHunter', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/osmahmoud/slopehunter/issues

Datasets:

data_example - Simulated effects on quantitative incidence and prognosis traits

On CRAN:

2.10 score 1 stars 25 scripts 7 exports 66 dependencies

Last updated from:b0686fe0c7. Checks:7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	NOTE	182
source / vignettes	OK	206
linux-release-x86_64	NOTE	205
macos-release-arm64	NOTE	141
macos-oldrel-arm64	NOTE	149
windows-devel	NOTE	128
windows-release	NOTE	128
windows-oldrel	NOTE	124
wasm-release	OK	182

Exports:format_data harmonise_effects hunt LD_prune read_incidence read_prognosis SHadj

Dependencies:askpass base64enc bslib cachem cli cpp11 crosstalk curl data.table digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr ieugwasr isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr mclust memoise mime openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Help page	Topics
Simulated effects on quantitative incidence and prognosis traits	data_example
Check and download PLINK 1.90 executable suitable for the operating system, and return its path Inspired by https://github.com/MRCIEU/genetics.binaRies	download_plink
Format input data	format_data
Harmonise and format data for Slope-Hunter	harmonise_effects
Estimate collider bias	hunt
clump function using local plink binary and ld reference dataset This function is modified from: https://github.com/MRCIEU/ieugwasr/blob/master/R/ld_clump.R	ld_local
Perform LD pruning on SNP data	LD_prune
Plotting model for Slope-Hunter clustering	plot.SH
Read incidence data	read_incidence
Read prognosis data	read_prognosis
Correct index event bias for new data	SHadj
Implement the EM algorithm for the SlopeHunter model-based clustering	shclust

Package: SlopeHunter 1.1.0

SlopeHunter: Slope-Hunter: A ROBUST METHOD FOR COLLIDER BIAS CORRECTION IN CONDITIONAL GENOME-WIDE ASSOCIATION STUDIES

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)