Skip to content

important update for new release #108

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
gaow merged 1 commit into from
Sep 9, 2025
Merged

important update for new release #108

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 7 additions & 4 deletions R/colocboost_check_update_jk.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,8 @@ boost_check_update_jk_nofocal <- function(cb_model, cb_model_para, cb_data) {
return(ifelse(length(jk_temp) == 1, jk_temp, sample(jk_temp, 1)))
})
update_jk[c(1, pos.update + 1)] <- c(jk, jk_each)


judge_each <- check_jk_jkeach(jk, jk_each,
pos.update,
model_update = model_update,
Expand Down Expand Up @@ -493,12 +495,12 @@ get_LD_jk1_jk2 <- function(jk1, jk2,
remain_jk = NULL) {
if (!is.null(X)) {
LD_temp <- suppressWarnings({
cor(X[, c(jk1, jk2)])
get_cormat(X[, c(jk1, jk2)])
})
LD_temp[which(is.na(LD_temp))] <- 0
LD_temp <- LD_temp[1, 2]
} else if (!is.null(XtX)) {
if (sum(XtX) == 1){
if (length(XtX) == 1){
LD_temp <- 0
} else {
jk1.remain <- which(remain_jk == jk1)
Expand Down Expand Up @@ -545,8 +547,9 @@ check_pair_jkeach <- function(jk_each,
jk_equiv_loglik = 0.001) {
data_update <- cb_data$data[pos.update]
# -- check if jk_i ~ jk_j
change_each_pair <- matrix(NA, nrow = length(jk_each), ncol = length(jk_each))
change_each_pair <- matrix(FALSE, nrow = length(jk_each), ncol = length(jk_each))
for (i in 1:length(jk_each)) {

jk_i <- jk_each[i]
change_log_jk_i <- model_update[[i]]$change_loglike[jk_i]
for (j in 1:length(jk_each)) {
Expand Down Expand Up @@ -597,7 +600,7 @@ estimate_change_profile_res <- function(jk,
} else {
xty <- XtY / scaling_factor
}
if (sum(xtx) == 1){
if (length(xtx) == 1){
rtr <- yty - 2 * sum(beta_k * xty) + sum(beta_k^2)
} else {
rtr <- yty - 2 * sum(beta_k * xty) + sum((xtx %*% as.matrix(beta_k)) * beta_k)
Expand Down
8 changes: 4 additions & 4 deletions R/colocboost_inference.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -241,7 +241,7 @@ check_null_post <- function(cb_obj,
} else {
xty <- XtY / scaling_factor
}
if (sum(xtx) == 1){
if (length(xtx) == 1){
(yty - 2 * sum(cs_beta * xty) + sum(cs_beta^2)) * adj_dep
} else {
(yty - 2 * sum(cs_beta * xty) + sum((xtx %*% as.matrix(cs_beta)) * cs_beta)) * adj_dep
Expand Down Expand Up @@ -293,14 +293,14 @@ check_null_post <- function(cb_obj,
if (length(miss_idx) != 0) {
xty <- XtY[-miss_idx] / scaling.factor
res.tmp <- rep(0, length(XtY))
if (sum(xtx) == 1){
if (length(xtx) == 1){
res.tmp[-miss_idx] <- xty - cs_beta[-miss_idx] / beta_scaling
} else {
res.tmp[-miss_idx] <- xty - xtx %*% (cs_beta[-miss_idx] / beta_scaling)
}
} else {
xty <- XtY / scaling.factor
if (sum(xtx) == 1){
if (length(xtx) == 1){
res.tmp <- xty - (cs_beta / beta_scaling)
} else {
res.tmp <- xty - xtx %*% (cs_beta / beta_scaling)
Expand Down Expand Up @@ -508,7 +508,7 @@ get_cos_evidence <- function(cb_obj, coloc_out, data_info) {
} else {
xty <- XtY / scaling_factor
}
if (sum(xtx) == 1){
if (length(xtx) == 1){
cos_profile <- (yty - 2 * sum(cs_beta * xty) + sum(cs_beta^2)) * adj_dep
} else {
cos_profile <- (yty - 2 * sum(cs_beta * xty) + sum((xtx %*% as.matrix(cs_beta)) * cs_beta)) * adj_dep
Expand Down
2 changes: 1 addition & 1 deletion R/colocboost_init.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -396,7 +396,7 @@ get_correlation <- function(X = NULL, res = NULL, XtY = NULL, N = NULL,
Xtr <- res / scaling_factor
XtY <- XtY / scaling_factor
}
if (sum(XtX) == 1){
if (length(XtX) == 1){
var_r <- YtY - 2 * sum(beta_k * XtY) + sum(beta_k^2)
} else {
var_r <- YtY - 2 * sum(beta_k * XtY) + sum((XtX %*% as.matrix(beta_k)) * beta_k)
Expand Down
8 changes: 4 additions & 4 deletions R/colocboost_update.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ colocboost_update <- function(cb_model, cb_model_para, cb_data) {
if (length(cb_data$data[[i]]$variable_miss) != 0) {
beta <- cb_model[[i]]$beta[-cb_data$data[[i]]$variable_miss] / beta_scaling
xty <- cb_data$data[[i]]$XtY[-cb_data$data[[i]]$variable_miss]
if (sum(xtx) == 1){
if (length(xtx) == 1){
cb_model[[i]]$res[-cb_data$data[[i]]$variable_miss] <- xty - scaling_factor * beta
} else {
cb_model[[i]]$res[-cb_data$data[[i]]$variable_miss] <- xty - scaling_factor * xtx %*% beta
Expand All @@ -120,7 +120,7 @@ colocboost_update <- function(cb_model, cb_model_para, cb_data) {
} else {
beta <- cb_model[[i]]$beta / beta_scaling
xty <- cb_data$data[[i]]$XtY
if (sum(xtx) == 1){
if (length(xtx) == 1){
cb_model[[i]]$res <- xty - scaling_factor * beta
} else {
cb_model[[i]]$res <- xty - scaling_factor * xtx %*% beta
Expand All @@ -129,7 +129,7 @@ colocboost_update <- function(cb_model, cb_model_para, cb_data) {
# - profile-loglikelihood
yty <- cb_data$data[[i]]$YtY / scaling_factor
xty <- xty / scaling_factor
if (sum(xtx) == 1){
if (length(xtx) == 1){
profile_log <- (yty - 2 * sum(beta * xty) + sum(beta^2)) * adj_dep
} else {
profile_log <- (yty - 2 * sum(beta * xty) + sum((xtx %*% as.matrix(beta)) * beta)) * adj_dep
Expand All @@ -152,7 +152,7 @@ get_LD_jk <- function(jk1, X = NULL, XtX = NULL, N = NULL, remain_idx = NULL, P
} else if (!is.null(XtX)) {
jk1.remain <- which(remain_idx == jk1)
corr <- rep(0, P)
if (sum(XtX) == 1 | length(jk1.remain)==0){
if (length(XtX) == 1 | length(jk1.remain)==0){
corr[remain_idx] <- 1
} else {
corr[remain_idx] <- XtX[, jk1.remain]
Expand Down