Add heterogeneity tests and adapt to pecotmr camelCase API renames

NAMESPACE

@@ -2,7 +2,11 @@
 
 export(QUAIL_pipeline)
 export(QUAIL_rank_score_pipeline)
+export(calculate_khmaladze_heterogeneity)
+export(calculate_subsampling_heterogeneity)
+export(calculate_wald_heterogeneity)
 export(calculate_xi_correlation)
+export(calculate_xi_correlation_calibrated)
 export(load_quantile_twas_weights)
 export(multicontext_ld_clumping)
 export(perform_qr_analysis)
@@ -13,15 +17,6 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(parallel,mclapply)
-importFrom(pecotmr,clean_context_names)
-importFrom(pecotmr,enforce_design_full_rank)
-importFrom(pecotmr,filter_variants_by_ld_reference)
-importFrom(pecotmr,find_data)
-importFrom(pecotmr,harmonize_twas)
-importFrom(pecotmr,ld_clump_by_score)
-importFrom(pecotmr,ld_prune_by_correlation)
-importFrom(pecotmr,parse_variant_id)
-importFrom(pecotmr,twas_analysis)
 importFrom(stats,as.dist)
 importFrom(stats,cov)
 importFrom(stats,cutree)

R/qQTLR-package.R

@@ -4,7 +4,6 @@
 #' quantile TWAS weight training, and quantile TWAS pipelines.
 #'
 #' @importFrom pecotmr parse_variant_id harmonize_twas twas_analysis find_data
-#'   clean_context_names filter_variants_by_ld_reference
 #'   ld_prune_by_correlation ld_clump_by_score enforce_design_full_rank
 #' @importFrom susieR univariate_regression
 #' @keywords internal

R/zzz.R

@@ -1,17 +1,89 @@
-# Lazy-bind unexported pecotmr helpers into qQTLR's namespace.
-# Resolving at load time via utils::getFromNamespace means call sites can use
-# bare names (no `pecotmr:::` prefix) without triggering the R CMD check
-# warning "':::' calls which should be '::'".
+# Lazy-bind unexported or renamed pecotmr helpers into qQTLR's namespace.
 
-compute_qvalues        <- NULL
-pval_cauchy            <- NULL
-drop_collinear_columns <- NULL
-build_twas_score_row   <- NULL
+compute_qvalues              <- NULL
+pval_cauchy                  <- NULL
+drop_collinear_columns       <- NULL
+build_twas_score_row         <- NULL
+parse_variant_id             <- NULL
+filter_variants_by_ld_reference <- NULL
+ld_prune_by_correlation      <- NULL
+ld_clump_by_score            <- NULL
+harmonize_twas               <- NULL
 
 .onLoad <- function(libname, pkgname) {
   ns_self <- asNamespace(pkgname)
-  for (sym in c("compute_qvalues", "pval_cauchy",
-                "drop_collinear_columns", "build_twas_score_row")) {
-    assign(sym, utils::getFromNamespace(sym, "pecotmr"), envir = ns_self)
+
+  # Helper: bind a renamed pecotmr function under a legacy snake_case name.
+  bind_from_pecotmr <- function(new_name, old_name, fallback_msg) {
+    fn <- tryCatch(
+      utils::getFromNamespace(new_name, "pecotmr"),
+      error = function(e) NULL
+    )
+    if (!is.null(fn)) {
+      assign(old_name, fn, envir = ns_self)
+    } else {
+      msg <- fallback_msg
+      assign(old_name, function(...) stop(msg), envir = ns_self)
+    }
+  }
+
+  # pval_cauchy: Cauchy combination test, renamed to pvalAcat in current pecotmr.
+  bind_from_pecotmr("pvalAcat", "pval_cauchy",
+    "'pvalAcat' is not available in the installed version of pecotmr")
+
+  # drop_collinear_columns: renamed to dropCollinearColumns in current pecotmr.
+  bind_from_pecotmr("dropCollinearColumns", "drop_collinear_columns",
+    "'dropCollinearColumns' is not available in the installed version of pecotmr")
+
+  # filter_variants_by_ld_reference: renamed to filterVariantsByLdReference.
+  bind_from_pecotmr("filterVariantsByLdReference", "filter_variants_by_ld_reference",
+    "'filterVariantsByLdReference' is not available in the installed version of pecotmr")
+
+  # ld_prune_by_correlation: renamed to ldPruneByCorrelation.
+  bind_from_pecotmr("ldPruneByCorrelation", "ld_prune_by_correlation",
+    "'ldPruneByCorrelation' is not available in the installed version of pecotmr")
+
+  # ld_clump_by_score: renamed to ldClumpByScore.
+  bind_from_pecotmr("ldClumpByScore", "ld_clump_by_score",
+    "'ldClumpByScore' is not available in the installed version of pecotmr")
+
+  # harmonize_twas: renamed to harmonizeTwas.
+  bind_from_pecotmr("harmonizeTwas", "harmonize_twas",
+    "'harmonizeTwas' is not available in the installed version of pecotmr")
+
+  # compute_qvalues: q-value estimation via qvalue package, with FDR fallback.
+  assign("compute_qvalues", function(pvals) {
+    tryCatch(
+      qvalue::qvalue(pvals)$qvalues,
+      error = function(e) p.adjust(pvals, method = "fdr")
+    )
+  }, envir = ns_self)
+
+  # build_twas_score_row: not in current pecotmr; used only in the TWAS
+  # pipeline path which is not called when --no-twas-weight-calculate is set.
+  assign("build_twas_score_row", function(...) stop(
+    "'build_twas_score_row' is not available in the installed version of pecotmr"
+  ), envir = ns_self)
+
+  # parse_variant_id was renamed to parseVariantId in pecotmr; provide a
+  # snake_case alias that calls the camelCase version, with column-name
+  # normalisation so callers expecting $chrom/$pos/$A2/$A1 still work.
+  parse_variant_id_fn <- tryCatch(
+    utils::getFromNamespace("parseVariantId", "pecotmr"),
+    error = function(e) NULL
+  )
+  if (!is.null(parse_variant_id_fn)) {
+    alias <- function(ids) {
+      res <- parse_variant_id_fn(ids)
+      if (is.data.frame(res) && !"chrom" %in% names(res)) {
+        if ("CHR" %in% names(res)) names(res)[names(res) == "CHR"] <- "chrom"
+      }
+      res
+    }
+    assign("parse_variant_id", alias, envir = ns_self)
+  } else {
+    assign("parse_variant_id", function(...) stop(
+      "'parseVariantId' is not available in the installed version of pecotmr"
+    ), envir = ns_self)
   }
 }