improve finemappingresult and website

DESCRIPTION

@@ -89,11 +89,11 @@ VignetteBuilder: knitr
 Config/roxygen2/version: 8.0.0
 RoxygenNote: 7.3.3
 Collate:
-    'allGenerics.R'
+    'AllGenerics.R'
+    'GenotypeHandle.R'
+    'AllClasses.R'
     'AnnotationMatrix.R'
     'FineMappingEntry.R'
-    'FineMappingResultBase.R'
-    'GenotypeHandle.R'
     'tupleSelectors.R'
     'GwasFineMappingResult.R'
     'H2Estimate.R'
@@ -105,14 +105,12 @@ Collate:
     'QtlDataset.R'
     'MultiStudyQtlDataset.R'
     'QtlFineMappingResult.R'
-    'SumStatsBase.R'
     'TwasWeightsEntry.R'
     'causalInferencePipeline.R'
     'colocPipeline.R'
     'colocboostPipeline.R'
     'cpp11.R'
     'ctwasPipeline.R'
-    'ctwasWrapper.R'
     'deprecated.R'
     'exampleData.R'
     'fineMappingPipeline.R'
@@ -121,7 +119,6 @@ Collate:
     'gwasSumStats.R'
     'h2Annotations.R'
     'h2EstimationWrappers.R'
-    'jointDispatchers.R'
     'jointSpecification.R'
     'ld.R'
     'mashPipeline.R'

NAMESPACE

@@ -93,7 +93,6 @@ export(getCs)
 export(getCtwasMetaData)
 export(getCvPerformance)
 export(getDataType)
-export(getEffects)
 export(getEigenList)
 export(getEnrichment)
 export(getFineMappingResult)
@@ -105,17 +104,16 @@ export(getGenotypeHandle)
 export(getGenotypes)
 export(getH2)
 export(getInSample)
-export(getLbf)
 export(getLdBlocks)
 export(getLdMatrixList)
 export(getLdScoreWeights)
 export(getLdScores)
 export(getLdSketch)
 export(getLocal)
 export(getMaf)
+export(getMarginalEffects)
 export(getMethodNames)
 export(getMixtureWeights)
-export(getMolecularId)
 export(getN)
 export(getNRef)
 export(getNSamples)
@@ -140,16 +138,15 @@ export(getStandardized)
 export(getStudy)
 export(getSumStats)
 export(getSumstatDf)
+export(getSusieFit)
 export(getSusieResult)
 export(getTauBlocks)
 export(getTopLoci)
 export(getTraits)
-export(getTrimmedFit)
 export(getTwasWeights)
 export(getVarY)
 export(getVariantIds)
 export(getVariantInfo)
-export(getVariantNames)
 export(getWeights)
 export(getZ)
 export(glmnetWeights)
@@ -243,7 +240,6 @@ export(susieInfWeights)
 export(susieRssPipeline)
 export(susieRssWeights)
 export(susieWeights)
-export(trimCtwasVariants)
 export(twasMultivariateWeightsPipeline)
 export(twasPipeline)
 export(twasPredict)
@@ -298,6 +294,7 @@ exportMethods(getLdScores)
 exportMethods(getLdSketch)
 exportMethods(getLocal)
 exportMethods(getMaf)
+exportMethods(getMarginalEffects)
 exportMethods(getMethodNames)
 exportMethods(getMixtureWeights)
 exportMethods(getN)
@@ -323,10 +320,10 @@ exportMethods(getStandardized)
 exportMethods(getStudy)
 exportMethods(getSumStats)
 exportMethods(getSumstatDf)
+exportMethods(getSusieFit)
 exportMethods(getTauBlocks)
 exportMethods(getTopLoci)
 exportMethods(getTraits)
-exportMethods(getTrimmedFit)
 exportMethods(getTwasWeights)
 exportMethods(getVarY)
 exportMethods(getVariantIds)

R/AllClasses.R

@@ -0,0 +1,125 @@
+# =============================================================================
+# AllClasses.R
+# -----------------------------------------------------------------------------
+# Virtual base classes shared across the package. Concrete subclasses live
+# in their own per-class files (QtlSumStats.R, GwasSumStats.R, QtlDataset.R,
+# QtlFineMappingResult.R, GwasFineMappingResult.R, etc.).
+#
+# Per Bioconductor convention this file is loaded first in the Collate
+# ordering (the "AllClasses.R" filename sorts to the top of the alphabet),
+# and every method-bearing file uses `@include AllClasses.R` so roxygen
+# topologically orders the Collate field for us.
+# =============================================================================
+
+#' @include AllGenerics.R GenotypeHandle.R
+#' @importFrom methods setClass setMethod new is validObject
+NULL
+
+# =============================================================================
+# SumStatsBase
+# -----------------------------------------------------------------------------
+# Shared parent of the QTL and GWAS summary statistics collections.
+# Concrete subclasses (QtlSumStats, GwasSumStats) inherit from DFrame and
+# share the ldSketch / genome / qcInfo slots. Class-specific accessors
+# (getZ / getN / getMaf / nSnps / subsetChr / getVarY / getSumStats)
+# stay on the concrete subclass because they rely on the tuple shape
+# (3-tuple for QtlSumStats, 1-tuple for GwasSumStats).
+# =============================================================================
+
+#' @title Summary Statistics Base Class
+#' @description Virtual base class for QTL and GWAS summary statistics
+#'   collections. Concrete subclasses (\code{QtlSumStats},
+#'   \code{GwasSumStats}) inherit from \code{DFrame} and share the
+#'   \code{ldSketch} / \code{genome} / \code{qcInfo} slots.
+#' @slot ldSketch The \code{GenotypeHandle} the QC pipeline harmonized
+#'   against. Required: \code{summaryStatsQc()} sets it.
+#' @slot genome Character, genome build label.
+#' @slot qcInfo A \code{list} recording which QC steps ran. Empty
+#'   \code{list()} on construction; populated by \code{summaryStatsQc()}
+#'   with a per-step audit record (filter names, drop counts, liftover
+#'   target, RAISS settings, etc.). Fine-mapping and TWAS-weights
+#'   pipelines reject inputs where \code{length(getQcInfo(x)) == 0L} — the
+#'   slot serves as both the gating flag and the audit trail.
+#' @export
+setClass("SumStatsBase",
+  contains = c("VIRTUAL", "DFrame"),
+  representation(
+    ldSketch = "GenotypeHandle",
+    genome   = "character",
+    qcInfo   = "list"
+  ))
+
+#' @rdname getGenome
+#' @export
+setMethod("getGenome", "SumStatsBase", function(x, ...) x@genome)
+
+#' @rdname getQcInfo
+#' @export
+setMethod("getQcInfo", "SumStatsBase", function(x, ...) x@qcInfo)
+
+#' @rdname getLdSketch
+#' @export
+setMethod("getLdSketch", "SumStatsBase", function(x, ...) x@ldSketch)
+
+#' @rdname getStudy
+#' @export
+setMethod("getStudy", "SumStatsBase",
+          function(x) unique(as.character(x$study)))
+
+# =============================================================================
+# FineMappingResultBase
+# -----------------------------------------------------------------------------
+# Shared parent of the QTL and GWAS fine-mapping result collections.
+# Concrete subclasses (QtlFineMappingResult, GwasFineMappingResult) carry
+# a DFrame of per-fit rows plus a shared ldSketch slot. Downstream
+# pipelines dispatch on FineMappingResultBase for behaviors that apply to
+# either flavour, and on the concrete subclass when the tuple shape
+# matters.
+# =============================================================================
+
+#' @title Fine-Mapping Result Base Class
+#' @description Virtual base class for fine-mapping result collections.
+#'   Concrete subclasses (\code{QtlFineMappingResult},
+#'   \code{GwasFineMappingResult}) carry a \code{DFrame} of per-fit rows
+#'   and a shared \code{ldSketch} slot. Downstream pipelines should
+#'   dispatch on \code{FineMappingResultBase} for behaviors that apply to
+#'   either flavour, and on the concrete subclass when the tuple shape
+#'   matters.
+#' @slot ldSketch The LD reference \code{GenotypeHandle} the fits were
+#'   computed against, or \code{NULL} when the fits were derived from
+#'   individual-level data (no LD reference). Used downstream for
+#'   cross-pipeline LD-sketch identity validation.
+#' @export
+setClass("FineMappingResultBase",
+  contains = c("VIRTUAL", "DFrame"),
+  representation(ldSketch = "ANY"))
+
+#' @rdname getStudy
+#' @export
+setMethod("getStudy", "FineMappingResultBase",
+          function(x) unique(as.character(x$study)))
+
+#' @rdname getLdSketch
+#' @export
+setMethod("getLdSketch", "FineMappingResultBase",
+          function(x, ...) x@ldSketch)
+
+#' @rdname getMethodNames
+#' @export
+setMethod("getMethodNames", "FineMappingResultBase",
+          function(x) unique(as.character(x$method)))
+
+#' @rdname adjustPips
+#' @export
+setMethod("adjustPips", "FineMappingResultBase",
+  function(x, keepVariants, ...) {
+    if (nrow(x) == 0L) return(x)
+    entries <- x@listData$entry
+    for (i in seq_along(entries)) {
+      adj <- tryCatch(adjustPips(entries[[i]], keepVariants, ...),
+                      error = function(err) NULL)
+      if (!is.null(adj)) entries[[i]] <- adj
+    }
+    x@listData$entry <- entries
+    x
+  })

R/allGenerics.R → R/AllGenerics.R

@@ -366,35 +366,54 @@ setGeneric("adjustPips",
 #' @export
 setGeneric("getPip", function(x, ...) standardGeneric("getPip"))
 
-#' @title Get Trimmed Fit
-#' @description Extract the trimmed SuSiE fit.
+#' @title Get SuSiE Fit
+#' @description Extract the SuSiE fit object from a fine-mapping entry
+#'   or result. The fit may be the trimmed view (when the pipeline ran
+#'   with the default \code{trim = TRUE}) or the full untrimmed
+#'   \code{susie()} return (when \code{trim = FALSE}).
 #' @param x A \code{FineMappingEntry} or \code{FineMappingResult}.
 #' @param ... Class-specific selection arguments.
-#' @return A list (trimmed SuSiE fit).
+#' @return A list (the SuSiE fit object).
 #' @export
-setGeneric("getTrimmedFit", function(x, ...) standardGeneric("getTrimmedFit"))
+setGeneric("getSusieFit", function(x, ...) standardGeneric("getSusieFit"))
 
-#' @title Get Variant Names
-#' @description Extract variant names.
-#' @param x A \code{FineMappingResult} object.
+#' @title Get Marginal Effects
+#' @description Extract per-variant marginal univariate effects from a
+#'   fine-mapping entry or result. Returns a \code{data.frame} with
+#'   identity columns (\code{variant_id, chrom, pos, A1, A2}), context
+#'   (\code{N, MAF}), and the marginal effect columns
+#'   (\code{beta, se, z, p}). Populated uniformly across the
+#'   individual-level and RSS paths.
+#' @param x A \code{FineMappingEntry} or \code{FineMappingResult}.
+#' @param maxPval Optional numeric (length 1). When non-\code{NULL},
+#'   filter rows where \code{p > maxPval}. Default \code{NULL}
+#'   (no filter).
 #' @param ... Class-specific selection arguments.
-#' @return Character vector of variant names.
+#' @return A \code{data.frame}.
 #' @export
-setGeneric("getVariantNames",
-  function(x, ...) standardGeneric("getVariantNames"))
-
-#' @title Get Top Loci
-#' @description Extract the top-loci payload as either a
-#'   \code{data.frame} (default, the on-disk shape) or a \code{GRanges}
-#'   (parsed from the \code{variant_id} \code{chr:pos:A2:A1} encoding,
-#'   with the remaining columns carried into \code{mcols}).
+setGeneric("getMarginalEffects",
+  function(x, maxPval = NULL, ...) standardGeneric("getMarginalEffects"))
+
+#' @title Get Top Loci (posterior view)
+#' @description Extract the per-variant posterior fine-mapping payload
+#'   as either a \code{data.frame} (default) or a \code{GRanges}.
+#'   Returns identity columns (\code{variant_id, chrom, pos, A1, A2}),
+#'   context (\code{N, MAF}), the posterior effect columns
+#'   (\code{beta = posterior_mean, se = posterior_sd}), \code{pip},
+#'   and credible-set membership columns (\code{cs_95}, etc.).
+#'   Rows are filtered by PIP by default — set \code{signalCutoff = 0}
+#'   to return every variant.
 #' @param x A \code{FineMappingEntry} or \code{FineMappingResult}.
 #' @param type One of \code{"data.frame"} (default) or \code{"GRanges"}.
+#' @param signalCutoff Numeric (length 1). Drop rows where
+#'   \code{pip <= signalCutoff}. Default \code{0.025}. Use
+#'   \code{signalCutoff = 0} to keep every variant.
 #' @param ... Class-specific selection arguments.
 #' @return A \code{data.frame} or a \code{GRanges}.
 #' @export
 setGeneric("getTopLoci",
-  function(x, type = c("data.frame", "GRanges"), ...)
+  function(x, type = c("data.frame", "GRanges"),
+           signalCutoff = 0.025, ...)
     standardGeneric("getTopLoci"))
 
 #' @title Get Credible Sets
@@ -405,23 +424,6 @@ setGeneric("getTopLoci",
 #' @export
 setGeneric("getCs", function(x, ...) standardGeneric("getCs"))
 
-#' @title Get Log Bayes Factors
-#' @description Extract per-variant log Bayes factors from a fine-mapping result.
-#' @param x A \code{FineMappingEntry} or \code{FineMappingResult}.
-#' @param ... Class-specific selection arguments.
-#' @return A data.frame with columns \code{variant_id} and one numeric column
-#'   per effect.
-#' @export
-setGeneric("getLbf", function(x, ...) standardGeneric("getLbf"))
-
-#' @title Get Per-Effect Fine-Mapping Summary
-#' @description Extract per-effect information from a fine-mapping result.
-#' @param x A \code{FineMappingEntry} or \code{FineMappingResult}.
-#' @param ... Class-specific selection arguments.
-#' @return A data.frame with one row per effect.
-#' @export
-setGeneric("getEffects", function(x, ...) standardGeneric("getEffects"))
-
 # =============================================================================
 # TwasWeights accessor generics
 # =============================================================================
@@ -468,16 +470,6 @@ setGeneric("getFits", function(x, ...) standardGeneric("getFits"))
 #' @export
 setGeneric("getMethodNames", function(x) standardGeneric("getMethodNames"))
 
-#' @title Get Molecular ID (legacy)
-#' @description Legacy accessor. The molecular identifier is now stored
-#'   as the \code{trait} column on \code{TwasWeights} and
-#'   \code{FineMappingResult} collections — use \code{getTraits(x)}
-#'   instead.
-#' @param x The object.
-#' @return Character vector.
-#' @export
-setGeneric("getMolecularId", function(x) standardGeneric("getMolecularId"))
-
 #' @title Get Data Type
 #' @description Extract the data-type tag.
 #' @param x A \code{TwasWeightsEntry} or \code{TwasWeights}.

R/AnnotationMatrix.R

@@ -6,7 +6,7 @@
 # baseline (always jointly fitted) or candidate (score-tested).
 # =============================================================================
 
-#' @include allGenerics.R
+#' @include AllGenerics.R
 NULL
 
 #' @title Genomic Annotation Matrix