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minor fix #37

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Merged
xueweic merged 1 commit into from
Apr 15, 2025
Merged

minor fix #37

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6 changes: 3 additions & 3 deletions R/colocboost.R
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Original file line number Diff line number Diff line change
Expand Up @@ -501,7 +501,7 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
min_variables <- min(sapply(keep_variables, length))
if (min_variables < 100){
warning("Warning message about the number of variables.\n",
"The smallest number of variables across outcomes is ", min_variables, "<100.",
"The smallest number of variables across outcomes is ", min_variables, "< 100.",
" If this is what you expected, this is not a problem.",
" If this is not what you expected, please check input data.")
}
Expand All @@ -513,8 +513,8 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
warning("Warning message about the overlapped variables.\n",
"The average number of variables across outcomes is ", mean_variables,
". But only ", length(overlapped_variables), " number of variables overlapped (<10%).\n",
"If this is what you expected, this is not a problem.\n",
"If this is not you expected, please check if the variable name matched across outcomes.")
" If this is what you expected, this is not a problem.",
" If this is not what you expected, please check if the variable name matched across outcomes.")
}
cb_data <- colocboost_init_data(X = X, Y = Y, dict_YX = yx_dict,
Z = Z, LD = LD, N_sumstat = N_sumstat, dict_sumstatLD = sumstatLD_dict,
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12 changes: 6 additions & 6 deletions R/colocboost_output.R
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Expand Up @@ -142,19 +142,19 @@ get_strong_colocalization <- function(cb_output,
return(cb_output)
} else {
if (is.null(pvalue_cutoff)){
message(paste("Extracting colocalization results with cos_npc_cutoff =", cos_npc_cutoff, "and npc_outcome_cutoff =", npc_outcome_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that the npc_outcome >", npc_outcome_cutoff, "."))
message(paste0("Extracting colocalization results with cos_npc_cutoff = ", cos_npc_cutoff, " and npc_outcome_cutoff = ", npc_outcome_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that the npc_outcome > ", npc_outcome_cutoff, "."))
} else {
if (pvalue_cutoff>1 | pvalue_cutoff<0){
warnings("Please check the pvalue cutoff in [0,1].")
return(cb_output)
}
if (npc_outcome_cutoff == 0 && cos_npc_cutoff == 0){
message(paste("Extracting colocalization results with pvalue_cutoff =", pvalue_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that pvalue of variants for the outcome <", pvalue_cutoff, "."))
message(paste0("Extracting colocalization results with pvalue_cutoff = ", pvalue_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that pvalue of variants for the outcome < ", pvalue_cutoff, "."))
} else {
message(paste("Extracting colocalization results with pvalue_cutoff =", pvalue_cutoff, ", cos_npc_cutoff =", cos_npc_cutoff, ", and npc_outcome_cutoff =", npc_outcome_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that pvalue of variants for the outcome <", pvalue_cutoff, " and npc_outcome >", npc_outcome_cutoff, "."))
message(paste0("Extracting colocalization results with pvalue_cutoff = ", pvalue_cutoff, ", cos_npc_cutoff = ", cos_npc_cutoff, ", and npc_outcome_cutoff = ", npc_outcome_cutoff, ".\n",
"For each CoS, keep the outcomes configurations that pvalue of variants for the outcome < ", pvalue_cutoff, " and npc_outcome >", npc_outcome_cutoff, "."))
}
}
}
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