get_cos_summary: Get colocalization summary table from a ColocBoost output.

In colocboost: Multi-Context Colocalization Analysis for QTL and GWAS Studies

Get colocalization summary table from a ColocBoost output.

Description

get_cos_summary get the colocalization summary table with or without the outcomes of interest.

Usage

get_cos_summary(
  cb_output,
  outcome_names = NULL,
  interest_outcome = NULL,
  region_name = NULL
)

Arguments

cb_output	Output object from colocboost analysis
outcome_names	Optional vector of names of outcomes, which has the same order as Y in the original analysis.
interest_outcome	Optional vector specifying a subset of outcomes from outcome_names to focus on. When provided, only colocalization events that include at least one of these outcomes will be returned.
region_name	Optional character string. When provided, adds a column with this gene name to the output table for easier filtering in downstream analyses.

Value

A summary table for colocalization events with the following columns:

focal_outcome	The focal outcome being analyzed if exists. Otherwise, it is FALSE.
colocalized_outcomes	Colocalized outcomes for colocalization confidence set (CoS)
cos_id	Unique identifier for colocalization confidence set (CoS)
purity	Minimum absolute correlation of variables with in colocalization confidence set (CoS)
top_variable	The variable with highest variant colocalization probability (VCP)
top_variable_vcp	Variant colocalization probability for the top variable
cos_npc	Normalized probability of colocalization
min_npc_outcome	Minimum normalized probability of colocalized traits
n_variables	Number of variables in colocalization confidence set (CoS)
colocalized_index	Indices of colocalized variables
colocalized_variables	List of colocalized variables
colocalized_variables_vcp	Variant colocalization probabilities for all colocalized variables

Source

See detailed instructions in our tutorial portal: https://statfungen.github.io/colocboost/articles/Interpret_ColocBoost_Output.html

See Also

Other colocboost_utilities: get_cormat(), get_cos(), get_cos_purity(), get_hierarchical_clusters(), get_ucos_summary()

Examples

# colocboost example
set.seed(1)
N <- 1000
P <- 100
# Generate X with LD structure
sigma <- 0.9^abs(outer(1:P, 1:P, "-"))
X <- MASS::mvrnorm(N, rep(0, P), sigma)
colnames(X) <- paste0("SNP", 1:P)
L <- 3
true_beta <- matrix(0, P, L)
true_beta[10, 1] <- 0.5 # SNP10 affects trait 1
true_beta[10, 2] <- 0.4 # SNP10 also affects trait 2 (colocalized)
true_beta[50, 2] <- 0.3 # SNP50 only affects trait 2
true_beta[80, 3] <- 0.6 # SNP80 only affects trait 3
Y <- matrix(0, N, L)
for (l in 1:L) {
  Y[, l] <- X %*% true_beta[, l] + rnorm(N, 0, 1)
}
res <- colocboost(X = X, Y = Y)
get_cos_summary(res)

colocboost documentation built on June 8, 2025, 11:07 a.m.