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Merged
xueweic merged 3 commits into from
Apr 20, 2025
Merged

monor changes #64

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6dbc829
Update colocboost_output.R
xueweic Apr 19, 2025
df10c94
minor change
xueweic Apr 20, 2025
3b923a3
Merge branch 'StatFunGen:main' into main
xueweic Apr 20, 2025
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4 changes: 3 additions & 1 deletion R/colocboost_output.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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.")
Expand Down Expand Up @@ -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 {
Expand All @@ -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, "."
))
}
Expand Down