fix RSS issues

NAMESPACE

@@ -134,8 +134,11 @@ export(getGenome)
 export(getGenotypeCovariates)
 export(getGenotypes)
 export(getH2)
+export(getH2Se)
 export(getImissCutoff)
 export(getInSample)
+export(getIntercept)
+export(getInterceptSe)
 export(getKeepIndel)
 export(getKeepVariants)
 export(getLbf)
@@ -153,6 +156,7 @@ export(getMethodNames)
 export(getMixtureWeights)
 export(getN)
 export(getNRef)
+export(getNSnps)
 export(getP)
 export(getPhenotypeCovariates)
 export(getPhenotypes)
@@ -181,6 +185,7 @@ export(getSusieFit)
 export(getSusieResult)
 export(getTauBlocks)
 export(getTopLoci)
+export(getTraitName)
 export(getTraitNames)
 export(getTraitPosition)
 export(getTraitRun)
@@ -365,8 +370,11 @@ exportMethods(getGenome)
 exportMethods(getGenotypeCovariates)
 exportMethods(getGenotypes)
 exportMethods(getH2)
+exportMethods(getH2Se)
 exportMethods(getImissCutoff)
 exportMethods(getInSample)
+exportMethods(getIntercept)
+exportMethods(getInterceptSe)
 exportMethods(getKeepIndel)
 exportMethods(getKeepVariants)
 exportMethods(getLbf)
@@ -384,6 +392,7 @@ exportMethods(getMethodNames)
 exportMethods(getMixtureWeights)
 exportMethods(getN)
 exportMethods(getNRef)
+exportMethods(getNSnps)
 exportMethods(getP)
 exportMethods(getPhenotypeCovariates)
 exportMethods(getPhenotypes)
@@ -402,7 +411,6 @@ exportMethods(getScoreStats)
 exportMethods(getSe)
 exportMethods(getSignificantQtls)
 exportMethods(getSnpIdx)
-exportMethods(getSnpInfo)
 exportMethods(getStandardized)
 exportMethods(getStudy)
 exportMethods(getSumStats)
@@ -411,6 +419,7 @@ exportMethods(getSusieAlpha)
 exportMethods(getSusieFit)
 exportMethods(getTauBlocks)
 exportMethods(getTopLoci)
+exportMethods(getTraitName)
 exportMethods(getTraitNames)
 exportMethods(getTraitPosition)
 exportMethods(getTraitRun)
@@ -552,6 +561,7 @@ importFrom(purrr,
   map_dfr,
   map_int,
   map_lgl,
+  partial,
   reduce,
   set_names
 )

R/AllGenerics.R

@@ -1162,9 +1162,14 @@ setGeneric("getFullFit", function(x, ...) standardGeneric("getFullFit"))
 setGeneric("getCvFits", function(x, ...) standardGeneric("getCvFits"))
 
 #' @title Get Method Names
-#' @description Extract method names from a collection class.
-#' @param x A \code{FineMappingResult} or \code{TwasWeights} object.
+#' @description Extract the method name(s) an object was produced with: one
+#'   per entry for a collection, a single name for one estimate.
+#' @param x A \code{FineMappingResult}, \code{TwasWeights},
+#'   \code{CtwasResult} or \code{H2Estimate} object.
 #' @return Character vector.
+#' @examples
+#' data(h2EstimateExample)
+#' getMethodNames(h2EstimateExample)
 #' @export
 setGeneric("getMethodNames", function(x) standardGeneric("getMethodNames"))
 
@@ -1441,9 +1446,16 @@ setGeneric("getScaleResiduals", function(x) {
 
 #' @title Get SNP Info
 #' @description Return the cached SNP metadata data.frame (columns: SNP, CHR,
-#'   BP, A1, A2, optionally MAF).
+#'   BP, A1, A2, fileIdx, optionally MAF).
 #' @param x An object carrying cached SNP metadata.
 #' @return A data.frame.
+#' @details The genotype handle is the seed layer behind a panel and
+#'   is not part of the public interface; obtain a panel from
+#'   \code{readGenotypes()} and ask it directly. This table is the READ-PATH
+#'   view: unlike the panel's \code{rowRanges()} it carries \code{fileIdx},
+#'   the on-disk variant position that keeps reads correct after a handle has
+#'   been row-subset. Callers that only need chrom/pos/alleles should use
+#'   \code{rowRanges()} on the panel instead.
 #' @keywords internal
 setGeneric("getSnpInfo", function(x) standardGeneric("getSnpInfo"))
 
@@ -1708,6 +1720,61 @@ setGeneric("getTauBlocks", function(x) standardGeneric("getTauBlocks"))
 #' @export
 setGeneric("getH2", function(x) standardGeneric("getH2"))
 
+#' @title Get Heritability Standard Error
+#' @description Return the standard error of the global SNP heritability
+#'   estimate carried by an \code{H2Estimate}.
+#' @param x An \code{H2Estimate}.
+#' @return Numeric (length 1).
+#' @examples
+#' data(h2EstimateExample)
+#' getH2Se(h2EstimateExample)
+#' @export
+setGeneric("getH2Se", function(x) standardGeneric("getH2Se"))
+
+#' @title Get LD-Score Regression Intercept
+#' @description Return the regression intercept carried by an
+#'   \code{H2Estimate}. Values above 1 indicate confounding or sample overlap
+#'   rather than polygenic signal.
+#' @param x An \code{H2Estimate}.
+#' @return Numeric (length 1).
+#' @examples
+#' data(h2EstimateExample)
+#' getIntercept(h2EstimateExample)
+#' @export
+setGeneric("getIntercept", function(x) standardGeneric("getIntercept"))
+
+#' @title Get Intercept Standard Error
+#' @description Return the standard error of the regression intercept carried
+#'   by an \code{H2Estimate}.
+#' @param x An \code{H2Estimate}.
+#' @return Numeric (length 1).
+#' @examples
+#' data(h2EstimateExample)
+#' getInterceptSe(h2EstimateExample)
+#' @export
+setGeneric("getInterceptSe", function(x) standardGeneric("getInterceptSe"))
+
+#' @title Get Variant Count
+#' @description Return the number of variants the heritability estimate was
+#'   computed over.
+#' @param x An \code{H2Estimate}.
+#' @return Integer (length 1).
+#' @examples
+#' data(h2EstimateExample)
+#' getNSnps(h2EstimateExample)
+#' @export
+setGeneric("getNSnps", function(x) standardGeneric("getNSnps"))
+
+#' @title Get Trait Name
+#' @description Return the trait label carried by an \code{H2Estimate}.
+#' @param x An \code{H2Estimate}.
+#' @return Character (length 1).
+#' @examples
+#' data(h2EstimateExample)
+#' getTraitName(h2EstimateExample)
+#' @export
+setGeneric("getTraitName", function(x) standardGeneric("getTraitName"))
+
 # Internal generics for the unified joint-analysis engine (see R/JointGroup.R
 # and dev/jointSpecification-s4-refactor.md). Not exported: the engine and its
 # fitters are package-internal machinery.

R/GenotypeHandle.R

@@ -680,7 +680,7 @@ GenotypeHandle <- function(
 }
 
 #' @rdname getSnpInfo
-#' @export
+#' @keywords internal
 setMethod("getSnpInfo", "GenotypeHandle", function(x) x@snpInfo)
 
 #' @rdname getFormat

R/H2Estimate.R

@@ -64,6 +64,30 @@ setClass(
 #' @export
 setMethod("getH2", "H2Estimate", function(x) x@h2)
 
+#' @rdname getH2Se
+#' @export
+setMethod("getH2Se", "H2Estimate", function(x) x@h2Se)
+
+#' @rdname getIntercept
+#' @export
+setMethod("getIntercept", "H2Estimate", function(x) x@intercept)
+
+#' @rdname getInterceptSe
+#' @export
+setMethod("getInterceptSe", "H2Estimate", function(x) x@interceptSe)
+
+#' @rdname getNSnps
+#' @export
+setMethod("getNSnps", "H2Estimate", function(x) x@nSnps)
+
+#' @rdname getTraitName
+#' @export
+setMethod("getTraitName", "H2Estimate", function(x) x@traitName)
+
+#' @rdname getMethodNames
+#' @export
+setMethod("getMethodNames", "H2Estimate", function(x) x@method)
+
 #' @rdname getTauBlocks
 #' @export
 setMethod("getTauBlocks", "H2Estimate", function(x) x@tauBlocks)

R/JointGroup.R

@@ -65,7 +65,7 @@ setClass(
 setClass(
     "IndividualJointGroup",
     contains = "JointGroup",
-    representation(X = "matrix", Y = "matrix", pos = "numeric"),
+    representation(X = "matrix", Y = "matrix", traitPos = "numeric"),
     validity = function(object) {
         errors <- character()
         if (nrow(object@X) != nrow(object@Y)) {
@@ -74,10 +74,16 @@ setClass(
         if (ncol(object@Y) != nrow(object@conditions)) {
             errors <- c(errors, "ncol(Y) must equal nrow(conditions)")
         }
-        if (length(object@pos) > 0L && length(object@pos) != ncol(object@Y)) {
+        if (
+            length(object@traitPos) > 0L &&
+                length(object@traitPos) != ncol(object@Y)
+        ) {
             errors <- c(
                 errors,
-                "when set, 'pos' must have one entry per Y column"
+                str_c(
+                    "when set, 'traitPos' must have one entry per TRAIT ",
+                    "(Y column), not per variant"
+                )
             )
         }
         if (length(errors) == 0L) TRUE else errors
@@ -88,21 +94,26 @@ setClass(
 setClass(
     "SumStatsJointGroup",
     contains = "JointGroup",
-    representation(Z = "matrix", R = "matrix", N = "numeric"),
+    # The LD REFERENCE, not the LD matrix: R is variants x variants, and
+    # every group in an enumeration would hold its own dense copy long before
+    # any of them is fitted. The sketch is a lazy panel, so the matrix is
+    # derived once per group at fit time -- which is what the univariate RSS
+    # path in fineMappingPipeline already does.
+    representation(Z = "matrix", ldSketch = "LdSketchOrNULL", N = "numeric"),
     validity = function(object) {
         errors <- character()
-        if (nrow(object@R) != ncol(object@R)) {
-            errors <- c(errors, "'R' (LD) must be square")
+        if (ncol(object@Z) != nrow(object@conditions)) {
+            errors <- c(errors, "ncol(Z) must equal nrow(conditions)")
         }
-        if (nrow(object@Z) != nrow(object@R)) {
+        if (is.null(rownames(object@Z))) {
             errors <- c(
                 errors,
-                "'Z' rows (variants) must match the 'R' dimension"
+                str_c(
+                    "'Z' must carry the variant ids as rownames: they are ",
+                    "what the LD matrix is derived over"
+                )
             )
         }
-        if (ncol(object@Z) != nrow(object@conditions)) {
-            errors <- c(errors, "ncol(Z) must equal nrow(conditions)")
-        }
         if (length(errors) == 0L) TRUE else errors
     }
 )
@@ -159,14 +170,36 @@ setClass("TwasJointPipeline", contains = "JointPipeline")
 # @noRd
 .jgY <- function(g) g@Y
 
+# The genomic midpoint of each TRAIT, one per Y column -- fsusie's functional
+# domain coordinate, not a variant position. Named apart from `pos`, which
+# everywhere else in the package means the position of a variant.
 # @noRd
-.jgPos <- function(g) g@pos
+.jgTraitPos <- function(g) g@traitPos
 
 # @noRd
 .jgZ <- function(g) g@Z
 
 # @noRd
-.jgR <- function(g) g@R
+.jgLdSketch <- function(g) g@ldSketch
+
+# The variants a summary-statistics group covers, in Z's row order -- which is
+# the order the derived LD matrix comes back in.
+# @noRd
+.jgVariantIds <- function(g) rownames(.jgZ(g))
+
+# The group's LD matrix, derived from its sketch.
+#
+# Callers must derive ONCE per group and pass the result down: the per-
+# condition entry builder runs once per Z column, so calling this from there
+# would recompute the same matrix for every condition.
+# @noRd
+.jgLdMatrix <- function(g) {
+    .ldFromSketch(
+        .jgLdSketch(g),
+        .jgVariantIds(g),
+        label = "jointEngine"
+    )
+}
 
 # @noRd
 .jgN <- function(g) g@N