Multi-Context Colocalization Analysis for QTL and GWAS Studies


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Documentation for package ‘colocboost’ version 1.0.4

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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