fix fsusie issues

NAMESPACE

@@ -95,6 +95,7 @@ export(MrmashOptions)
 export(MrmashPriorParam)
 export(MrmashRssOptions)
 export(MultiStudyQtlDataset)
+export(MvsusieMixturePriorOptions)
 export(MvsusieOptions)
 export(MvsusieRssOptions)
 export(NcvregOptions)
@@ -157,6 +158,7 @@ export(blockMetadata)
 export(buildLdEigen)
 export(buildLdScore)
 export(buildMrmashPriorMatrices)
+export(buildMvsusieMixturePrior)
 export(buildTopLoci)
 export(calculateFeatureScores)
 export(causalInferencePipeline)
@@ -220,19 +222,18 @@ export(fineMappingResult)
 export(fineMappingRow)
 export(finemapCtwasRegions)
 export(fitFsusie)
+export(fitGlmnetCv)
 export(fitMashContrast)
 export(fitMvsusie)
 export(fitMvsusieRss)
 export(fitRetention)
-export(fitSusieInfThenSusieRss)
 export(flattenTupleRanges)
 export(formatFinemappingOutput)
 export(frqData)
 export(fsusieAffectedRegions)
 export(fsusieCredibleBand)
 export(fsusieGetCs)
 export(fsusieWeights)
-export(fsusieWrapper)
 export(fullFit)
 export(genomicRegion)
 export(genotypeCovariates)

R/MethodOptions.R

@@ -390,6 +390,36 @@ setClass("MethodOptions", contains = "SimpleList")
     ))
 }
 
+# Refuse names for a reason OTHER than pecotmr supplying them -- a name the
+# engine does not have, or one it has that pecotmr will not expose. Those
+# cannot go through .configRefuseOwned(), whose message promises the value
+# would be overwritten and names where to set it instead; here there is no
+# such place, so the reason is stated outright. `unavailable` is a named
+# character vector, name = the refused argument, value = why, read as
+# "`<name>` cannot be set here: <why>".
+#
+# This exists for engines taking `...`, where an unknown name is accepted and
+# silently ignored instead of reported (see .engineAcceptedNames). Everywhere
+# else the engine's own formals are the check.
+# @noRd
+.configRefuseUnavailable <- function(extra, unavailable, label) {
+    clash <- intersect(names(extra), names(unavailable))
+    if (length(clash) == 0L) {
+        return(invisible(NULL))
+    }
+    why <- str_flatten(
+        sprintf(
+            "`%s` cannot be set here: %s",
+            clash,
+            unname(
+                unavailable[clash]
+            )
+        ),
+        collapse = "; "
+    )
+    abort(glue("{label}: {why}."))
+}
+
 # TRUE for a record a constructor produced. Used by the pipelines to refuse a
 # bare list, which is the whole point of requiring constructors.
 # @noRd

R/fineMappingPipeline.R

@@ -1920,7 +1920,7 @@ combineFineMappingResults <- function(..., ldSketch = NULL) {
         return(.fmFoldWeightsMv(Xtr, Ytr, coverage, userArgs, mvPrior))
     }
     if (token == "fsusie") {
-        return(.fmFoldWeightsFsusie(Xtr, Ytr, pos, userArgs))
+        return(.fmFoldWeightsFsusie(Xtr, Ytr, pos, coverage, userArgs))
     }
     NULL
 }
@@ -1971,9 +1971,11 @@ combineFineMappingResults <- function(..., ldSketch = NULL) {
 
 # Per-fold fsusie weights.
 # @noRd
-.fmFoldWeightsFsusie <- function(Xtr, Ytr, pos, userArgs) {
+.fmFoldWeightsFsusie <- function(Xtr, Ytr, pos, coverage, userArgs) {
+    # coverage reaches the fold fit here for the same reason it does in the
+    # susie and mvsusie fold paths; L is left to susiF's default there too.
     fsArgs <- .fmMergeUserArgs(
-        list(X = Xtr, Y = Ytr, pos = pos),
+        list(X = Xtr, Y = Ytr, pos = pos, covLev = coverage),
         "fsusie",
         userArgs
     )
@@ -3501,14 +3503,18 @@ setMethod(
             ),
             csHome["coverage"]
         ),
+        # Only what the pipeline ACTUALLY supplies. `prior`, `max_scale` and
+        # `max_SNP_EM` used to be listed here because this row described the
+        # retired fsusieWrapper(), which passed them; the pipeline calls
+        # fitFsusie() and never did, so refusing them closed the only path to
+        # setting them at all -- the same trap the `residual_variance` note
+        # above records.
         "fsusieR::susiF" = c(
-            set_names(rep(fromData, 4L), c("X", "Y", "pos", "prior")),
+            set_names(rep(fromData, 3L), c("X", "Y", "pos")),
             c(
                 L = "`maxNumSingleEffects()` on CredibleSetParam",
-                min_purity = "the wrapper's `minPurity`",
-                max_SNP_EM = "the wrapper's `maxSnpEm`",
-                cov_lev = "the wrapper's `covLev`",
-                max_scale = "the wrapper's `maxScale`"
+                cov_lev = "`csCoverage()` on CredibleSetParam",
+                min_purity = "`minAbsCorr()` on CredibleSetParam"
             )
         ),
         character(0)