fix bug in predictSmooth #237

statOmics · Sep 19, 2023 · 38221e3 · 38221e3
1 parent ed2e8d6
commit 38221e3
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: tradeSeq
 Type: Package
 Title: trajectory-based differential expression analysis for sequencing data
 Date: 2019-03-17
-Version: 1.13.01
+Version: 1.13.02
 Authors@R: c(person("Koen", "Van den Berge", role = c("aut"),
                      email = "[email protected]"),
               person("Hector", "Roux de Bezieux", role = c("aut", "cre"),

diff --git a/R/fitGAM.R b/R/fitGAM.R
@@ -598,7 +598,7 @@ setMethod(f = "fitGAM",
 #' @rdname fitGAM
 #' @importClassesFrom Matrix dgCMatrix
 setMethod(f = "fitGAM",
-          signature = c(counts = "dgCMatrix"),
+          signature = c(counts = "generalMatrix"),
           definition = function(counts,
                                 sds = NULL,
                                 pseudotime = NULL,

diff --git a/R/predictSmooth.R b/R/predictSmooth.R
@@ -88,8 +88,8 @@ setOldClass("gam")
   yhatMat <- matrix(NA, nrow = length(gene), ncol = nCurves * nConditions * nPoints)
   rownames(yhatMat) <- gene
   pointNames <- expand.grid(1:nCurves, 1:nConditions)
-  baseNames <- paste0("lineage", pointNames[,1], "_condition",
-                      levels(conditions)[pointNames[,2]])
+  baseNames <- paste0("lineage", rep(1:nCurves, each=nConditions), "_condition",
+                      levels(conditions)[rep(1:nConditions, nCurves)])
   colnames(yhatMat) <- c(sapply(baseNames, paste0, "_point",1:nPoints))
   for (jj in 1:length(gene)) {
     yhat <- c(exp(t(Xall %*% t(beta[as.character(gene[jj]), ,