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Add X_ref parameter: accept reference panel genotype matrix instead of LD #134

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Add X_ref parameter: accept reference panel genotype matrix instead of LD #134

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28aab0e
Add X_ref - Code only
xueweic Apr 1, 2026
b539ca3
Add unit test for X-ref
xueweic Apr 1, 2026
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4 changes: 4 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,10 @@ export(get_hierarchical_clusters)
export(get_robust_colocalization)
export(get_robust_ucos)
export(get_ucos_summary)
importFrom(Rfast,correls)
importFrom(Rfast,med)
importFrom(Rfast,standardise)
importFrom(Rfast,upper_tri)
importFrom(grDevices,adjustcolor)
importFrom(graphics,abline)
importFrom(graphics,axis)
Expand Down
143 changes: 107 additions & 36 deletions R/colocboost.R
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5 changes: 4 additions & 1 deletion R/colocboost_assemble.R
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Expand Up @@ -132,10 +132,13 @@ colocboost_assemble <- function(cb_obj,
}
}
if (!is.null(cb_obj_single$cb_data$data[[1]][["XtY"]])) {
X_dict <- cb_obj$cb_data$dict[i]
if (is.null(cb_obj_single$cb_data$data[[1]]$XtX)) {
X_dict <- cb_obj$cb_data$dict[i]
cb_obj_single$cb_data$data[[1]]$XtX <- cb_obj$cb_data$data[[X_dict]]$XtX
}
if (is.null(cb_obj_single$cb_data$data[[1]]$ref_label)) {
cb_obj_single$cb_data$data[[1]]$ref_label <- cb_obj$cb_data$data[[X_dict]]$ref_label
}
}
class(cb_obj_single) <- "colocboost"
out_ucos_each <- colocboost_assemble_ucos(cb_obj_single,
Expand Down
18 changes: 12 additions & 6 deletions R/colocboost_assemble_cos.R
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Expand Up @@ -43,7 +43,8 @@ colocboost_assemble_cos <- function(cb_obj,
X = cb_data$data[[X_dict]]$X, Xcorr = cb_data$data[[X_dict]]$XtX,
N = cb_data$data[[coloc_outcomes[iiii]]]$N, n = n_purity, coverage = sec_coverage_thresh,
min_abs_corr = min_abs_corr, median_abs_corr = median_abs_corr,
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss,
ref_label = cb_data$data[[X_dict]]$ref_label
)
check_purity[iiii] <- length(tmp) == 1
}
Expand Down Expand Up @@ -83,7 +84,8 @@ colocboost_assemble_cos <- function(cb_obj,
p_tmp <- matrix(get_purity(pos,
X = cb_data$data[[X_dict]]$X,
Xcorr = cb_data$data[[X_dict]]$XtX,
N = cb_data$data[[i]]$N, n = n_purity
N = cb_data$data[[i]]$N, n = n_purity,
ref_label = cb_data$data[[X_dict]]$ref_label
), 1, 3)
purity <- c(purity, list(p_tmp))
}
Expand Down Expand Up @@ -148,7 +150,8 @@ colocboost_assemble_cos <- function(cb_obj,
X = cb_data$data[[X_dict]]$X, Xcorr = cb_data$data[[X_dict]]$XtX,
N = cb_data$data[[coloc_outcomes[iiii]]]$N, n = n_purity, coverage = sec_coverage_thresh,
min_abs_corr = min_abs_corr, median_abs_corr = median_abs_corr,
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss,
ref_label = cb_data$data[[X_dict]]$ref_label
)
check_purity[iiii] <- length(tmp) == 1
}
Expand Down Expand Up @@ -208,7 +211,8 @@ colocboost_assemble_cos <- function(cb_obj,
X = cb_data$data[[X_dict]]$X, Xcorr = cb_data$data[[X_dict]]$XtX,
N = cb_data$data[[coloc_outcomes[iiii]]]$N, n = n_purity, coverage = sec_coverage_thresh,
min_abs_corr = min_abs_corr, median_abs_corr = median_abs_corr,
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss
miss_idx = cb_data$data[[coloc_outcomes[iiii]]]$variable_miss,
ref_label = cb_data$data[[X_dict]]$ref_label
)
check_purity[[iiii]] <- tmp
}
Expand Down Expand Up @@ -351,7 +355,8 @@ colocboost_assemble_cos <- function(cb_obj,
X = cb_data$data[[X_dict]]$X,
Xcorr = cb_data$data[[X_dict]]$XtX,
miss_idx = cb_data$data[[i]]$variable_miss,
P = cb_model_para$P
P = cb_model_para$P,
ref_label = cb_data$data[[X_dict]]$ref_label
)
}
res <- Reduce(pmax, res)
Expand Down Expand Up @@ -438,7 +443,8 @@ colocboost_assemble_cos <- function(cb_obj,
tmp <- matrix(get_purity(pos,
X = cb_data$data[[X_dict]]$X,
Xcorr = cb_data$data[[X_dict]]$XtX,
N = cb_data$data[[i3]]$N, n = n_purity
N = cb_data$data[[i3]]$N, n = n_purity,
ref_label = cb_data$data[[X_dict]]$ref_label
), 1, 3)
p_tmp <- rbind(p_tmp, tmp)
}
Expand Down
12 changes: 8 additions & 4 deletions R/colocboost_assemble_ucos.R
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,8 @@ colocboost_assemble_ucos <- function(cb_obj_single,
}
purity <- matrix(get_purity(pos,
X = cb_data$data[[1]]$X, Xcorr = cb_data$data[[1]]$XtX,
N = cb_data$data[[1]]$N, n = n_purity
N = cb_data$data[[1]]$N, n = n_purity,
ref_label = cb_data$data[[1]]$ref_label
), 1, 3)
purity <- as.data.frame(purity)
colnames(purity) <- c("min_abs_corr", "mean_abs_corr", "median_abs_corr")
Expand Down Expand Up @@ -131,7 +132,8 @@ colocboost_assemble_ucos <- function(cb_obj_single,
X = cb_data$data[[1]]$X, Xcorr = cb_data$data[[1]]$XtX,
N = cb_data$data[[1]]$N, n = n_purity, coverage = coverage,
min_abs_corr = min_abs_corr, median_abs_corr = median_abs_corr,
miss_idx = cb_data$data[[1]]$variable_miss
miss_idx = cb_data$data[[1]]$variable_miss,
ref_label = cb_data$data[[1]]$ref_label
)
if (length(check_purity) != 0) {
w <- w[check_purity]
Expand Down Expand Up @@ -237,7 +239,8 @@ colocboost_assemble_ucos <- function(cb_obj_single,
X = cb_data$data[[1]]$X,
Xcorr = cb_data$data[[1]]$XtX,
miss_idx = cb_data$data[[1]]$variable_miss,
P = cb_model_para$P
P = cb_model_para$P,
ref_label = cb_data$data[[1]]$ref_label
)
min_between[i.between, j.between] <- min_between[j.between, i.between] <- res[1]
max_between[i.between, j.between] <- max_between[j.between, i.between] <- res[2]
Expand Down Expand Up @@ -301,7 +304,8 @@ colocboost_assemble_ucos <- function(cb_obj_single,
purity,
matrix(get_purity(pos,
X = cb_data$data[[1]]$X, Xcorr = cb_data$data[[1]]$XtX,
N = cb_data$data[[1]]$N, n = n_purity
N = cb_data$data[[1]]$N, n = n_purity,
ref_label = cb_data$data[[1]]$ref_label
), 1, 3)
)
}
Expand Down
57 changes: 41 additions & 16 deletions R/colocboost_check_update_jk.R
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Expand Up @@ -122,7 +122,9 @@ boost_check_update_jk_nofocal <- function(cb_model, cb_model_para, cb_data) {
YtY = data_update[[ii]]$YtY,
XtY = data_update[[ii]]$XtY,
beta_k = model_update[[ii]]$beta,
miss_idx = data_update[[ii]]$variable_miss
miss_idx = data_update[[ii]]$variable_miss,
ref_label = cb_data$data[[X_dict[ii]]]$ref_label,
XtX_beta_cache = model_update[[ii]]$XtX_beta_cache
)
})
change_res_each <- as.numeric(unlist(change_res_each))
Expand Down Expand Up @@ -197,7 +199,9 @@ boost_check_update_jk_nofocal <- function(cb_model, cb_model_para, cb_data) {
YtY = data_update[[ii]]$YtY,
XtY = data_update[[ii]]$XtY,
beta_k = model_update[[ii]]$beta,
miss_idx = data_update[[ii]]$variable_miss
miss_idx = data_update[[ii]]$variable_miss,
ref_label = cb_data$data[[X_dict[ii]]]$ref_label,
XtX_beta_cache = model_update[[ii]]$XtX_beta_cache
)
})
change_res_each <- as.numeric(unlist(change_res_each))
Expand Down Expand Up @@ -241,7 +245,9 @@ boost_check_update_jk_nofocal <- function(cb_model, cb_model_para, cb_data) {
YtY = data_update[[ii]]$YtY,
XtY = data_update[[ii]]$XtY,
beta_k = model_update[[ii]]$beta,
miss_idx = data_update[[ii]]$variable_miss
miss_idx = data_update[[ii]]$variable_miss,
ref_label = cb_data$data[[X_dict[ii]]]$ref_label,
XtX_beta_cache = model_update[[ii]]$XtX_beta_cache
)
})
change_res_each <- as.numeric(unlist(change_res_each))
Expand Down Expand Up @@ -368,7 +374,8 @@ boost_check_update_jk_focal <- function(cb_model, cb_model_para, cb_data,
X = cb_data$data[[X_dict[pp_focal]]]$X,
XtX = cb_data$data[[X_dict[pp_focal]]]$XtX,
N = cb_data$data[[X_dict[pp_focal]]]$N,
remain_jk = 1:cb_model_para$P
remain_jk = 1:cb_model_para$P,
ref_label = cb_data$data[[X_dict[pp_focal]]]$ref_label
)
})
# ----- second, if within the same LD buddies, select the following variants
Expand All @@ -379,7 +386,8 @@ boost_check_update_jk_focal <- function(cb_model, cb_model_para, cb_data,
# ----- third, if picked variant within the same LD buddies
ld_tmp <- get_LD_jk1_jk2(jk_focal, jk_focal_tmp,
XtX = cb_data$data[[X_dict[pp_focal]]]$XtX,
remain_jk = 1:cb_model_para$P
remain_jk = 1:cb_model_para$P,
ref_label = cb_data$data[[X_dict[pp_focal]]]$ref_label
)
if (ld_tmp > jk_equiv_corr) {
jk_focal <- jk_focal_tmp
Expand Down Expand Up @@ -491,20 +499,26 @@ boost_check_update_jk_focal <- function(cb_model, cb_model_para, cb_data,
#' @importFrom stats cor
get_LD_jk1_jk2 <- function(jk1, jk2,
X = NULL, XtX = NULL, N = NULL,
remain_jk = NULL) {
remain_jk = NULL, ref_label = "LD") {
if (!is.null(X)) {
LD_temp <- suppressWarnings({
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 (length(XtX) == 1){
if (identical(ref_label, "No_ref")) {
LD_temp <- 0
} else {
jk1.remain <- match(jk1, remain_jk)
jk2.remain <- match(jk2, remain_jk)
LD_temp <- XtX[jk1.remain, jk2.remain]
if (identical(ref_label, "X_ref")) {
LD_temp <- suppressWarnings({ get_cormat(XtX[, c(jk1.remain, jk2.remain)]) })
LD_temp[which(is.na(LD_temp))] <- 0
LD_temp <- LD_temp[1, 2]
} else {
LD_temp <- XtX[jk1.remain, jk2.remain]
}
}
}
return(LD_temp)
Expand All @@ -528,7 +542,8 @@ check_jk_jkeach <- function(jk, jk_each,
X = cb_data$data[[X_dict[i]]]$X,
XtX = cb_data$data[[X_dict[i]]]$XtX,
N = data_update[[i]]$N,
remain_jk = setdiff(1:length(model_update[[i]]$res), data_update[[i]]$variable_miss)
remain_jk = setdiff(1:length(model_update[[i]]$res), data_update[[i]]$variable_miss),
ref_label = cb_data$data[[X_dict[i]]]$ref_label
)
judge[i] <- (change_each <= jk_equiv_loglik) & (abs(LD_temp) >= jk_equiv_corr)
} else {
Expand All @@ -549,19 +564,23 @@ check_pair_jkeach <- function(jk_each,
#' @importFrom stats cor
get_LD_jk_each <- function(jk_each,
X = NULL, XtX = NULL, N = NULL,
remain_jk = NULL) {
remain_jk = NULL, ref_label = "LD") {
if (!is.null(X)) {
LD_temp <- suppressWarnings({
get_cormat(X[, jk_each])
})
LD_temp[which(is.na(LD_temp))] <- 0
# LD_temp <- LD_temp[1, 2]
} else if (!is.null(XtX)) {
if (length(XtX) == 1){
if (identical(ref_label, "No_ref")) {
LD_temp <- matrix(0, length(jk_each), length(jk_each))
} else {
jk.remain <- match(jk_each, remain_jk)
LD_temp <- XtX[jk.remain, jk.remain]
if (identical(ref_label, "X_ref")) {
LD_temp <- suppressWarnings({ get_cormat(XtX[, jk.remain]) })
} else {
LD_temp <- XtX[jk.remain, jk.remain]
}
LD_temp[which(is.na(LD_temp))] <- 0
}
}
Expand All @@ -582,7 +601,8 @@ check_pair_jkeach <- function(jk_each,
X = cb_data$data[[X_dict[idx]]]$X,
XtX = cb_data$data[[X_dict[idx]]]$XtX,
N = data_update[[idx]]$N,
remain_jk = setdiff(1:length(model_update[[idx]]$res), data_update[[idx]]$variable_miss)
remain_jk = setdiff(1:length(model_update[[idx]]$res), data_update[[idx]]$variable_miss),
ref_label = cb_data$data[[X_dict[idx]]]$ref_label
)
})

Expand Down Expand Up @@ -612,7 +632,9 @@ estimate_change_profile_res <- function(jk,
X = NULL, res = NULL, N = NULL,
XtX = NULL, YtY = NULL, XtY = NULL,
beta_k = NULL,
miss_idx = NULL) {
miss_idx = NULL,
ref_label = "LD",
XtX_beta_cache = NULL) {
if (!is.null(X)) {
rtr <- sum(res^2) / (N - 1)
xtr <- t(X[, jk]) %*% res / (N - 1)
Expand All @@ -629,10 +651,13 @@ estimate_change_profile_res <- function(jk,
} else {
xty <- XtY / scaling_factor
}
if (length(xtx) == 1){
if (identical(ref_label, "No_ref")) {
rtr <- yty - 2 * sum(beta_k * xty) + sum(beta_k^2)
} else if (!is.null(XtX_beta_cache)) {
rtr <- yty - 2 * sum(beta_k * xty) + sum(XtX_beta_cache * beta_k)
} else {
rtr <- yty - 2 * sum(beta_k * xty) + sum((xtx %*% as.matrix(beta_k)) * beta_k)
XtX_beta <- compute_XtX_product(xtx, beta_k, ref_label)
rtr <- yty - 2 * sum(beta_k * xty) + sum(XtX_beta * beta_k)
}
}
numerator <- xtr^2 / (2 * rtr)
Expand Down
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