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colocboost (version 1.0.7)

Multi-Context Colocalization Analysis for QTL and GWAS Studies

Description

A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects, based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS) and quantitative trait loci (QTL) studies. The ColocBoost model is described in Cao et. al. (2025) .

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install.packages('colocboost')

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155

Version

1.0.7

License

MIT + file LICENSE

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Maintainer

Xuewei Cao

Last Published

November 22nd, 2025

Functions in colocboost (1.0.7)

get_cos_purity

Calculate purity within and in-between CoS
get_hierarchical_clusters

Perform modularity-based hierarchical clustering for a correlation matrix
get_cos_summary

Get colocalization summary table from a ColocBoost output.
get_colocboost_summary

Get summary tables from a ColocBoost output.
get_robust_colocalization

Recalibrate and summarize robust colocalization events.
get_cos

Extract CoS at different coverage
get_ucos_summary

Get trait-specific summary table from a ColocBoost output.
get_cormat

A fast function to calculate correlation matrix (LD matrix) from individual level data
Non_Causal_Strongest_Marginal

Individual level data for 2 traits and 2 causal variants, but the strongest marginal association is not causal
colocboost

ColocBoost: A gradient boosting informed multi-omics xQTL colocalization method
get_ambiguous_colocalization

Get ambiguous colocalization events from trait-specific (uncolocalized) effects.
colocboost_plot

Plot visualization plot from a ColocBoost output.
colocboost_validate_input_data

Validate and Process All Input Data for ColocBoost
Ind_5traits

Individual level data for 5 traits
Heterogeneous_Effect

Individual level data for 2 traits and 2 causal variants with heterogeneous effects
Sumstat_5traits

Summary level data for 5 traits
Ambiguous_Colocalization

A real data example includes an ambiguous colocalization between eQTL and GWAS
Weaker_GWAS_Effect

Individual level data for 2 traits and 2 causal variants with weaker effects for focal trait