minor fix bugs

NAMESPACE

@@ -169,7 +169,6 @@ importFrom(stats,cor)
 importFrom(stats,cov)
 importFrom(stats,cutree)
 importFrom(stats,hclust)
-importFrom(stats,lag)
 importFrom(stats,lm.fit)
 importFrom(stats,pchisq)
 importFrom(stats,pnorm)

R/LD.R

@@ -7,6 +7,10 @@ check_consecutive_regions <- function(df) {
     as.integer(sub("^chr", "", df$chrom)), # Remove 'chr' and convert to integer
     as.integer(df$chrom)
   ) # Convert to integer if not already
+
+  # Remove duplicated rows based on 'chrom' and 'start' columns
+  df <- distinct(df, chrom, start, .keep_all = TRUE) %>%
+    arrange(chrom, start)
 
   for (chr in unique(df$chrom)) {
     chr_rows <- which(df$chrom == chr)
@@ -20,9 +24,6 @@ check_consecutive_regions <- function(df) {
     }
   }
 
-  # Remove duplicated rows based on 'chrom' and 'start' columns
-  df <- distinct(df, chrom, start, .keep_all = TRUE) %>%
-    arrange(chrom, start)
 
   return(df)
 }

R/RcppExports.R

@@ -2,21 +2,22 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 dentist_iterative_impute <- function(LD_mat, nSample, zScore, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, ncpus, seed, correct_chen_et_al_bug, verbose = FALSE) {
-  .Call("_pecotmr_dentist_iterative_impute", PACKAGE = "pecotmr", LD_mat, nSample, zScore, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, ncpus, seed, correct_chen_et_al_bug, verbose)
+    .Call('_pecotmr_dentist_iterative_impute', PACKAGE = 'pecotmr', LD_mat, nSample, zScore, pValueThreshold, propSVD, gcControl, nIter, gPvalueThreshold, ncpus, seed, correct_chen_et_al_bug, verbose)
 }
 
 rcpp_mr_ash_rss <- function(bhat, shat, z, R, var_y, n, sigma2_e, s0, w0, mu1_init, tol = 1e-8, max_iter = 1e5L, update_w0 = TRUE, update_sigma = TRUE, compute_ELBO = TRUE, standardize = FALSE, ncpus = 1L) {
-  .Call("_pecotmr_rcpp_mr_ash_rss", PACKAGE = "pecotmr", bhat, shat, z, R, var_y, n, sigma2_e, s0, w0, mu1_init, tol, max_iter, update_w0, update_sigma, compute_ELBO, standardize, ncpus)
+    .Call('_pecotmr_rcpp_mr_ash_rss', PACKAGE = 'pecotmr', bhat, shat, z, R, var_y, n, sigma2_e, s0, w0, mu1_init, tol, max_iter, update_w0, update_sigma, compute_ELBO, standardize, ncpus)
 }
 
 prs_cs_rcpp <- function(a, b, phi, bhat, maf, n, ld_blk, n_iter, n_burnin, thin, verbose, seed) {
-  .Call("_pecotmr_prs_cs_rcpp", PACKAGE = "pecotmr", a, b, phi, bhat, maf, n, ld_blk, n_iter, n_burnin, thin, verbose, seed)
+    .Call('_pecotmr_prs_cs_rcpp', PACKAGE = 'pecotmr', a, b, phi, bhat, maf, n, ld_blk, n_iter, n_burnin, thin, verbose, seed)
 }
 
 qtl_enrichment_rcpp <- function(r_gwas_pip, r_qtl_susie_fit, pi_gwas = 0, pi_qtl = 0, ImpN = 25L, shrinkage_lambda = 1.0, num_threads = 1L) {
-  .Call("_pecotmr_qtl_enrichment_rcpp", PACKAGE = "pecotmr", r_gwas_pip, r_qtl_susie_fit, pi_gwas, pi_qtl, ImpN, shrinkage_lambda, num_threads)
+    .Call('_pecotmr_qtl_enrichment_rcpp', PACKAGE = 'pecotmr', r_gwas_pip, r_qtl_susie_fit, pi_gwas, pi_qtl, ImpN, shrinkage_lambda, num_threads)
 }
 
 sdpr_rcpp <- function(bhat, LD, n, per_variant_sample_size = NULL, array = NULL, a = 0.1, c = 1.0, M = 1000L, a0k = 0.5, b0k = 0.5, iter = 1000L, burn = 200L, thin = 5L, n_threads = 1L, opt_llk = 1L, verbose = TRUE) {
-  .Call("_pecotmr_sdpr_rcpp", PACKAGE = "pecotmr", bhat, LD, n, per_variant_sample_size, array, a, c, M, a0k, b0k, iter, burn, thin, n_threads, opt_llk, verbose)
+    .Call('_pecotmr_sdpr_rcpp', PACKAGE = 'pecotmr', bhat, LD, n, per_variant_sample_size, array, a, c, M, a0k, b0k, iter, burn, thin, n_threads, opt_llk, verbose)
 }
+

R/raiss.R

@@ -131,10 +131,10 @@ raiss <- function(ref_panel, known_zscores, LD_matrix, lamb = 0.01, rcond = 0.01
 
   combine_with_boundary_check <- function(combined_result, new_result) {
     # If either is empty, simply return the non-empty one or empty data frame
-    if (nrow(combined_result) == 0) {
+    if (is.null(combined_result)) {
       return(new_result)
     }
-    if (nrow(new_result) == 0) {
+    if (is.null(new_result)) {
       return(combined_result)
     }