diff --git a/R/colocboost_output.R b/R/colocboost_output.R index 144cd8f..05b3dd4 100644 --- a/R/colocboost_output.R +++ b/R/colocboost_output.R @@ -116,7 +116,7 @@ get_cos_summary <- function(cb_output, tt <- sapply(interest_outcome, function(tmp) grep(paste0(tmp, "\\b"), cp)) all(sapply(tt, length) != 0) }) - summary_table$interest_outcome <- interest_outcome + summary_table$interest_outcome <- paste0(interest_outcome, collapse = "; ") summary_table <- summary_table[which(if.interest), ] if (sum(if.interest) == 0) { warning("No colocalization with interest outcomes.") @@ -204,6 +204,7 @@ get_robust_colocalization <- function(cb_output, if (is.null(pvalue_cutoff)) { message(paste0( "Extracting colocalization results with cos_npc_cutoff = ", cos_npc_cutoff, " and npc_outcome_cutoff = ", npc_outcome_cutoff, ".\n", + "Keep only CoS with cos_npc >= ", cos_npc_cutoff, ". ", "For each CoS, keep the outcomes configurations that the npc_outcome >= ", npc_outcome_cutoff, "." )) } else { @@ -219,6 +220,7 @@ get_robust_colocalization <- function(cb_output, } else { message(paste0( "Extracting colocalization results with pvalue_cutoff = ", pvalue_cutoff, ", cos_npc_cutoff = ", cos_npc_cutoff, ", and npc_outcome_cutoff = ", npc_outcome_cutoff, ".\n", + "Keep only CoS with cos_npc >= ", cos_npc_cutoff, ". ", "For each CoS, keep the outcomes configurations that pvalue of variants for the outcome < ", pvalue_cutoff, " and npc_outcome >", npc_outcome_cutoff, "." )) }