Multi-Context Colocalization Analysis for QTL and GWAS Studies

Documentation for package ‘colocboost’ version 1.0.4

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_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