Package index • colocboost

Example Data

Example datasets for demonstration and testing.

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

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

Ind_5traits: Individual level data for 5 traits

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

Sumstat_5traits: Summary level data for 5 traits

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

Model fitting

Main interface function for fitting multi-trait colocalization model.

colocboost(): ColocBoost: A gradient boosting informed multi-omics xQTL colocalization method

Inference and summary

Functions for inference and summary from fitted model.

get_robust_colocalization(): Recalibrate and summarize robust colocalization events.

get_colocboost_summary(): Get summary tables from a ColocBoost output.

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

Visualization

Functions for visualizing ColocBoost result.

colocboost_plot(): Plot visualization plot from a ColocBoost output.

Utilities

Helper functions and utilities

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

get_cos(): Extract CoS at different coverage

get_cos_purity(): Calculate purity within and in-between CoS

get_cos_summary(): Get colocalization summary table from a ColocBoost output.

get_hierarchical_clusters(): Perform modularity-based hierarchical clustering for a correlation matrix

get_ucos_summary(): Get trait-specific summary table from a ColocBoost output.