# Multi-Context Colocalization Analysis for QTL and GWAS Studies

## Documentation for package ‘colocboost’ version 1.0.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

Ambiguous_Colocalization | A real data example includes an ambiguous colocalization between eQTL and GWAS
colocboost | ColocBoost: A gradient boosting informed multi-omics xQTL colocalization method
colocboost_plot | Plot visualization plot from a ColocBoost output.
get_ambiguous_colocalization | Get ambiguous colocalization events from trait-specific (uncolocalized) effects.
get_colocboost_summary | Get summary tables from a ColocBoost output.
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_robust_colocalization | Recalibrate and summarize robust colocalization events.
get_robust_ucos | Recalibrate and summarize robust uncolocalized events.
get_ucos_summary | Get trait-specific summary table from a ColocBoost output.
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