From 88e53123adbcfbe2dc08f2ffeeafb928a9a712a6 Mon Sep 17 00:00:00 2001 From: xuewei cao <36172337+xueweic@users.noreply.github.com> Date: Tue, 15 Apr 2025 13:14:48 -0400 Subject: [PATCH] minor fix --- R/colocboost.R | 6 +++--- R/colocboost_output.R | 12 ++++++------ 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/R/colocboost.R b/R/colocboost.R index 029d0e0..d83dbe3 100644 --- a/R/colocboost.R +++ b/R/colocboost.R @@ -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.") } @@ -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, diff --git a/R/colocboost_output.R b/R/colocboost_output.R index 0e613a8..742596f 100644 --- a/R/colocboost_output.R +++ b/R/colocboost_output.R @@ -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, ".")) } } }