R-universe - chr1swallace (Chris Wallace)

coloc - Colocalisation Tests of Two Genetic Traits

Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>, Pullin and Wallace (2025) <doi:10.1101/2024.08.21.608957>.

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13.66 score 213 stars 3 dependents 1.8k scripts 7.8k downloads

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'.

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4.26 score 3 stars 12 scripts 427 downloads

genomic.autocorr - Models Dealing with Spatial Dependency in Genomic Data

Local structure in genomic data often induces dependence between observations taken at different genomic locations. Ignoring this dependence leads to underestimation of the standard error of parameter estimates. This package uses block bootstrapping to estimate asymptotically correct standard errors of parameters from any standard generalised linear model that may be fit by the glm() function.

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2.70 score 5 scripts 284 downloads