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release request #16

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Merged
gaow merged 1 commit into from
Mar 26, 2025
Merged

release request #16

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2 changes: 0 additions & 2 deletions R/colocboost.R
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Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,6 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
multicorrection_cut = 1,
ash_prior = "normal", # only applicable if func_multicorrection = lfsr
p.adjust.methods = "fdr",
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,
Expand Down Expand Up @@ -568,7 +567,6 @@ colocboost <- function(X = NULL, Y = NULL, # individual data
coverage = coverage,
func_intw = func_intw,
alpha = alpha,
npc_cutoff = npc_cutoff,
check_null = check_null,
check_null_method = check_null_method,
check_null_max = check_null_max,
Expand Down
3 changes: 1 addition & 2 deletions R/colocboost_assemble.R
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Expand Up @@ -26,7 +26,6 @@ colocboost_assemble <- function(cb_obj,
check_null = 0.1,
check_null_method = "profile",
check_null_max=2e-5,
npc_cutoff = 0.7,
dedup = TRUE,
overlap = TRUE,
n_purity = 100,
Expand Down Expand Up @@ -193,7 +192,7 @@ 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, npc_cutoff = npc_cutoff)
cos_results <- get_cos_details(cb_obj, coloc_out = past_out$cos$cos, data_info = data_info)
cb_output <- list("vcp" = cos_results$vcp,
"cos_details" = cos_results$cos_results,
"data_info" = data_info,
Expand Down
4 changes: 2 additions & 2 deletions R/colocboost_output.R
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Expand Up @@ -75,7 +75,7 @@ get_data_info <- function(cb_obj){

#' @noRd
#' @keywords cb_post_inference
get_cos_details <- function(cb_obj, coloc_out, data_info = NULL, npc_cutoff = 0.7){
get_cos_details <- function(cb_obj, coloc_out, data_info = NULL){

if (is.null(data_info))
data_info <- get_data_info(cb_obj)
Expand All @@ -86,7 +86,7 @@ get_cos_details <- function(cb_obj, coloc_out, data_info = NULL, npc_cutoff = 0.
if (length(coloc_sets)!=0){

# - colocalization outcome configurations
tmp <- get_cos_evidence(cb_obj, coloc_out, data_info, npc_cutoff = npc_cutoff)
tmp <- get_cos_evidence(cb_obj, coloc_out, data_info)
normalization_evidence <- tmp$normalization_evidence
npc <- tmp$npc

Expand Down
18 changes: 11 additions & 7 deletions R/colocboost_utils.R
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Expand Up @@ -339,7 +339,7 @@ get_between_purity = function (pos1, pos2, X=NULL, Xcorr=NULL, N = NULL, miss_id
}


get_cos_evidence <- function(cb_obj, coloc_out, data_info, npc_cutoff = 0.7){
get_cos_evidence <- function(cb_obj, coloc_out, data_info){

get_cos_config <- function(w, config_idx, alpha = 1.5, coverage = 0.95){

Expand Down Expand Up @@ -395,7 +395,7 @@ get_cos_evidence <- function(cb_obj, coloc_out, data_info, npc_cutoff = 0.7){
}

# - calculate best configuration likelihood explained by minimal configuration
get_normalization_evidence <- function(profile_change, null_max, outcomes, outcome_names, npc_cutoff = 0.7) {
get_normalization_evidence <- function(profile_change, null_max, outcomes, outcome_names) {
# Define the exponential likelihood ratio normalization (ELRN)
logLR_normalization <- function(ratio) { 1 - exp( - 2*ratio ) }

Expand All @@ -405,10 +405,16 @@ get_cos_evidence <- function(cb_obj, coloc_out, data_info, npc_cutoff = 0.7){
rownames(df) <- outcome_names[outcomes]
sorted_df <- df[order(-df$relative_logLR), ]
sorted_df$strong_effect <- sorted_df$relative_logLR >= 1
sorted_df$suggestive_effect <- sorted_df$npc_outcome >= npc_cutoff
return(sorted_df)
}

get_npuc <- function(npc_outcome){
# npuc_outcome <- sapply(1:length(npc_outcome), function(i) npc_outcome[i]*prod(1-npc_outcome[-i]) )
# 1 - prod(1-npuc_outcome)
max_idx <- which.max(npc_outcome)
npc_outcome[max_idx] * prod(1 - npc_outcome[-max_idx])
}

avWeight <- coloc_out$avWeight
cs_change <- coloc_out$cs_change
check_null_max <- sapply(cb_obj$cb_model, function(cb) cb$check_null_max)
Expand All @@ -426,12 +432,10 @@ get_cos_evidence <- function(cb_obj, coloc_out, data_info, npc_cutoff = 0.7){
})
normalization_evidence[[i]] <- get_normalization_evidence(profile_change = profile_change_outcome,
null_max = check_null_max[outcomes],
outcomes, outcome_names, npc_cutoff = npc_cutoff)
outcomes, outcome_names)

# - calcualte CoS colocalization probability (CCP) and CoS uncolocalization probability (UCCP)
npc_outcome <- normalization_evidence[[i]]$npc_outcome
max_idx <- which.max(npc_outcome)
npuc <- npc_outcome[max_idx] * prod(1 - npc_outcome[-max_idx])
npuc <- get_npuc(normalization_evidence[[i]]$npc_outcome)
npc[i] <- 1 - npuc
}
names(normalization_evidence) <- names(npc) <- names(coloc_out$cos)
Expand Down
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