get_colocboost_summary {colocboost}R Documentation

Get summary tables from a ColocBoost output.

Description

get_colocboost_summary get colocalization and trait-specific summary table with or without the outcomes of interest.

Usage

get_colocboost_summary(
  cb_output,
  summary_level = 1,
  outcome_names = NULL,
  interest_outcome = NULL,
  region_name = NULL,
  min_abs_corr_between_ucos = 0.5,
  median_abs_corr_between_ucos = 0.8
)

Arguments

cb_output

Output object from colocboost analysis

summary_level

When summary_level = 1, return basic summary table for colocalization results. See details in get_ucos_summary function when summary_level = 2.

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.

min_abs_corr_between_ucos

Minimum absolute correlation for variants across two trait-specific (uncolocalized) effects to be considered colocalized. The default is 0.5.

median_abs_corr_between_ucos

Median absolute correlation for variants across two trait-specific (uncolocalized) effects to be considered colocalized. The default is 0.8.

Details

When summary_level = 1, additional details and examples are introduced in get_cos_summary. When summary_level = 2 or summary_level = 3, additional details for trait-specific effects and ambiguous colocalization events are included. See get_ucos_summary for details on these tables.

Value

A list containing results from the ColocBoost analysis:

Source

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

See Also

Other colocboost_inference: get_ambiguous_colocalization(), get_robust_colocalization()

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_colocboost_summary(res)


[Package colocboost version 1.0.4 Index]