RSS fixes

NAMESPACE

@@ -125,6 +125,7 @@ export(getPgenPtr)
 export(getPhenotypeCovariates)
 export(getPhenotypes)
 export(getPip)
+export(getQcDiagnostics)
 export(getQcInfo)
 export(getQtlDatasets)
 export(getRefPanel)
@@ -232,6 +233,7 @@ export(screenCtwasRegions)
 export(sdpr)
 export(sdprWeights)
 export(slalom)
+export(sldscPostprocessingPipeline)
 export(sliceMashData)
 export(standardiseSumstatsColumns)
 export(standardizeSldscTrait)
@@ -309,6 +311,7 @@ exportMethods(getPgenPtr)
 exportMethods(getPhenotypeCovariates)
 exportMethods(getPhenotypes)
 exportMethods(getPip)
+exportMethods(getQcDiagnostics)
 exportMethods(getQcInfo)
 exportMethods(getQtlDatasets)
 exportMethods(getRefPanel)

R/AllClasses.R

@@ -57,6 +57,28 @@ setMethod("getGenome", "SumStatsBase", function(x, ...) x@genome)
 #' @export
 setMethod("getQcInfo", "SumStatsBase", function(x, ...) x@qcInfo)
 
+#' @rdname getQcDiagnostics
+#' @export
+setMethod("getQcDiagnostics", "SumStatsBase",
+  function(x, entry = 1L, ...) {
+    qc <- x@qcInfo
+    if (length(qc) == 0L) return(NULL)
+    audits <- qc$entryAudit
+    if (is.null(audits)) return(NULL)
+    if (is.null(entry)) {
+      out <- lapply(audits, function(a) a$ldMismatchDiagnostics)
+      keep <- !vapply(out, is.null, logical(1L))
+      if (!any(keep)) return(NULL)
+      setNames(out[keep], seq_along(audits)[keep])
+    } else {
+      if (!is.numeric(entry) || length(entry) != 1L ||
+          entry < 1L || entry > length(audits)) {
+        stop("`entry` must be a single integer in 1:", length(audits), ".")
+      }
+      audits[[as.integer(entry)]]$ldMismatchDiagnostics
+    }
+  })
+
 #' @rdname getLdSketch
 #' @export
 setMethod("getLdSketch", "SumStatsBase", function(x, ...) x@ldSketch)

R/AllGenerics.R

@@ -238,6 +238,26 @@ setGeneric("getGenome", function(x, ...) standardGeneric("getGenome"))
 #' @export
 setGeneric("getQcInfo", function(x, ...) standardGeneric("getQcInfo"))
 
+#' @title Get SLALOM / DENTIST Diagnostics
+#' @description Return the per-variant LD-mismatch diagnostics table
+#'   (SLALOM or DENTIST output) attached to a sumstats entry by
+#'   \code{\link{summaryStatsQc}} when \code{zMismatchQc} was not
+#'   \code{"none"}. Convenience accessor over
+#'   \code{getQcInfo(x)$entryAudit[[entry]]$ldMismatchDiagnostics}.
+#' @param x A \code{GwasSumStats} or \code{QtlSumStats} object.
+#' @param entry Integer index (default 1) of the entry whose diagnostics
+#'   table to return. When \code{NULL}, returns a named list of every
+#'   entry's diagnostics keyed by entry index.
+#' @param ... Unused.
+#' @return A \code{data.frame} of per-variant diagnostics (columns
+#'   include \code{variant_id} plus the SLALOM / DENTIST output
+#'   columns), \code{NULL} when no diagnostics were preserved for that
+#'   entry, or a named list of such data.frames when \code{entry =
+#'   NULL}.
+#' @export
+setGeneric("getQcDiagnostics",
+  function(x, entry = 1L, ...) standardGeneric("getQcDiagnostics"))
+
 #' @title Get LD Sketch
 #' @description Return the \code{GenotypeHandle} carrying the LD
 #'   reference for this collection. Defined on classes that embed an