Package: colocPropTest 0.9.1

Chris Wallace

colocPropTest: Proportional Testing for Colocalisation Analysis

Colocalisation analysis tests whether two traits share a causal genetic variant in a specified genomic region. Proportional testing for colocalisation has been previously proposed [Wallace (2013) <doi:10.1002/gepi.21765>], but is reimplemented here to overcome barriers to its adoption. Its use is complementary to the fine- mapping based colocalisation method in the 'coloc' package, and may be used in particular to identify false "H3" conclusions in 'coloc'.

Authors:Chris Wallace [aut, cre]

colocPropTest_0.9.1.tar.gz
colocPropTest_0.9.1.tar.gz(r-4.5-noble)colocPropTest_0.9.1.tar.gz(r-4.4-noble)
colocPropTest_0.9.1.tgz(r-4.4-emscripten)colocPropTest_0.9.1.tgz(r-4.3-emscripten)
colocPropTest.pdf |colocPropTest.html✨
colocPropTest/json (API)

# Install 'colocPropTest' in R:

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 3 scripts 554 downloads 6 exports 72 dependencies

Last updated 7 months agofrom:8cbd07caf7. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 09 2024
R-4.5-linux	OK	Dec 09 2024

Exports:adjust_LD estprop lp plot_ellipses run_proptests tag

Dependencies:abind backports boot broom car carData cli coloc colorspace cowplot cpp11 crayon data.table Deriv doBy dplyr fansi farver Formula generics ggplot2 glue gridExtra gtable irlba isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels matrixStats mgcv microbenchmark minqa mixsqp modelr munsell nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig plyr purrr quantreg R6 RColorBrewer Rcpp RcppArmadillo RcppEigen reshape rlang scales SparseM stringi stringr survival susieR tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr

Proportional colocalisation

Chris Wallace

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Dec 09 2024.

Last update: 2024-06-12
Started: 2024-06-12

Help page	Topics
adjust LD for variable sample size	adjust_LD
Proportional colocalisation testing supplying only a pair of regression coefficients.	estprop
Proportional colocalisation testing	estprop_slow
keep snp subset of coloc dataset	keep_from_S
logp	lp
create variance-covariance matrix for pair of marginal beta + vbeta, given estimate of r between snps	marg_with_V
Helper function to adjust LD parameter r for differential sample size between snps	nform
draw two ellipses	plot_ellipses
run proportional tests on extreme subset of snp pairs from two coloc style datasets. Of all functions in this package, this is the main one that should be used.	run_proptests
Derive tag SNPs using heirarchical clustering	tag
run proportional test directly on marginal test stats from coloc datasets	tester_marg

Package: colocPropTest 0.9.1

colocPropTest: Proportional Testing for Colocalisation Analysis

Proportional colocalisation

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Usage by other packages (reverse dependencies)