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adding npc and fixed several bugs #15

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Merged
gaow merged 2 commits into from
Mar 22, 2025
Merged

adding npc and fixed several bugs #15

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0d5c782
adding npc
xueweic Mar 22, 2025
17ddac2
package code update
xueweic Mar 22, 2025
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6 changes: 4 additions & 2 deletions R/colocboost.R
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Original file line number Diff line number Diff line change
Expand Up @@ -157,12 +157,13 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
multicorrection_cut = 1,
ash_prior = "normal", # only applicable if func_multicorrection = lfsr
p.adjust.methods = "fdr",
pv_cutoff = 1e-4,
npc_cutoff = 0.7,
check_null = 0.1, # the cut off value for change conditional objective function
check_null_method = "profile",
check_null_max = 0.02,
residual_correlation = NULL, # sample overlap, it is diagonal if it is NULL
LD_obj = FALSE,
dynamic_step = TRUE,
weaker_ucos = TRUE,
output_level = 1){

Expand Down Expand Up @@ -557,6 +558,7 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
func_compare = func_compare,
coloc_thres = coloc_thres,
LD_obj = LD_obj,
dynamic_step = dynamic_step,
target_idx = target_idx,
outcome_names = outcome_names)

Expand All @@ -566,7 +568,7 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
coverage = coverage,
func_intw = func_intw,
alpha = alpha,
pv_cutoff = pv_cutoff,
npc_cutoff = npc_cutoff,
check_null = check_null,
check_null_method = check_null_method,
check_null_max = check_null_max,
Expand Down
7 changes: 4 additions & 3 deletions R/colocboost_addhoc_utils.R
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Expand Up @@ -61,8 +61,8 @@ merge_cos_ucos <- function(cb_obj, out_cos, out_ucos, coverage = 0.95,
min_between <- res[1]
max_between <- res[2]
ave_between <- res[3]
# is.between <- ((min_between>min_abs_corr) & (abs(max_between-1) < tol))
is.between <- (min_between>min_abs_corr) * (abs(max_between-1)<tol) * (ave_between>between_purity)
is.between <- ((min_between>between_purity) & (abs(max_between-1) < tol))
# is.between <- (min_between>min_abs_corr) * (abs(max_between-1)<tol) * (ave_between>between_purity)
if (is.between){
is_overlap = c(is_overlap, j)
# -- add weight
Expand Down Expand Up @@ -154,7 +154,8 @@ merge_ucos <- function(cb_obj, past_out,
ave_between[i.between, j.between] <- ave_between[j.between, i.between] <- res[3]
}
}
is.between <- (min_between>min_abs_corr) * (abs(max_between-1)<tol) * (ave_between>between_purity)
# is.between <- (min_between>min_abs_corr) * (abs(max_between-1)<tol) * (ave_between>between_purity)
is.between <- ((min_between>between_purity) & (abs(max_between-1) < tol))
if (sum(is.between) != 0){
temp <- sapply(1:nrow(is.between), function(x){
tt <- c(x, which(is.between[x,] != 0))
Expand Down
10 changes: 4 additions & 6 deletions R/colocboost_assemble.R
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Expand Up @@ -26,7 +26,7 @@ colocboost_assemble <- function(cb_obj,
check_null = 0.1,
check_null_method = "profile",
check_null_max=2e-5,
pv_cutoff = 1e-4,
npc_cutoff = 0.7,
dedup = TRUE,
overlap = TRUE,
n_purity = 100,
Expand Down Expand Up @@ -193,10 +193,7 @@ colocboost_assemble <- function(cb_obj,
# - colocalization results
cb_obj$cb_model_para$alpha <- alpha
cb_obj$cb_model_para$coverage <- coverage
cos_results <- get_cos_details(cb_obj, coloc_out = past_out$cos$cos, data_info = data_info)
if (!is.null(pv_cutoff) & !is.null(cos_results$cos_results)){
cos_results <- cos_pvalue_filter(cos_results, data_info = data_info, pv_cutoff = pv_cutoff)
}
cos_results <- get_cos_details(cb_obj, coloc_out = past_out$cos$cos, data_info = data_info, npc_cutoff = npc_cutoff)
cb_output <- list("vcp" = cos_results$vcp,
"cos_details" = cos_results$cos_results,
"data_info" = data_info,
Expand All @@ -210,7 +207,8 @@ colocboost_assemble <- function(cb_obj,

# - save model and all coloc and single information for diagnostic
if (output_level != 1){
tmp <- get_full_output(cb_obj = cb_obj, past_out = past_out, variables = data_info$variables, cb_output = cb_output)
tmp <- get_full_output(cb_obj = cb_obj, past_out = past_out, variables = data_info$variables,
cb_output = cb_output)
if (output_level == 2){
cb_output <- c(cb_output, list("ucos_details" = tmp$ucos_details))
cb_output <- cb_output[c("cos_summary", "vcp", "cos_details", "data_info", "model_info", "ucos_details")]
Expand Down
4 changes: 2 additions & 2 deletions R/colocboost_assemble_cos.R
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Expand Up @@ -180,8 +180,8 @@ colocboost_assemble_cos <- function(cb_obj,

} else {

av <- lapply(coloc_outcomes, function(i){
get_avWeigth(cb_model, i, update, pos.coloc[pos_temp_coloc_each])
av <- lapply(coloc_outcomes, function(ii){
get_avWeigth(cb_model, ii, update, pos.coloc[pos_temp_coloc_each])
})
weight_coloc <- do.call(cbind, av)

Expand Down
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