Merge branch 'main' of https://github.com/bigomics/playbase

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: playbase
 Type: Package
 Title: Core back-end functionality and logic for OmicsPlayground
-Version: 0.1.55
+Version: 0.1.57
 Author: BigOmics Analytics SA
 Maintainer: The package maintainer <[email protected]>
 Description: More about what it does (maybe more than one line)

R/gset-meta.r

@@ -172,7 +172,7 @@ gset.fitContrastsWithAllMethods <- function(gmt,
       if (nmissing > 0) {
         message("Found ", nmissing, " missing values in X. Removing prior to GSVA::ssgsea.")
       }
-      zx.ssgsea <- try(GSVA::gsva(as.matrix(X[complete.cases(X), ]),
+      zx.ssgsea <- try(GSVA::gsva(as.matrix(X[complete.cases(X), , drop = FALSE]),
         gmt[],
         method = "ssgsea",
         parallel.sz = mc.cores,

R/pgx-compute.R

@@ -904,22 +904,24 @@ pgx.add_GMT <- function(pgx, custom.geneset = NULL, max.genesets = 20000) {
     # get the length of go.genesets and add to gmt info
     go.size <- sapply(go.genesets, length)
 
-    # convert to sparse matrix
-    go.gmt <- playbase::createSparseGenesetMatrix(
-      gmt.all = go.genesets,
-      min.geneset.size = 15,
-      max.geneset.size = 400,
-      all_genes = full_feature_list,
-      min_gene_frequency = 1,
-      annot = pgx$genes,
-      filter_genes = FALSE
-    )
+    if (length(go.size) > 0) { # if no go genesets pass the min/max filter playbase function crashes
+      # convert to sparse matrix
+      go.gmt <- playbase::createSparseGenesetMatrix(
+        gmt.all = go.genesets,
+        min.geneset.size = 15,
+        max.geneset.size = 400,
+        all_genes = full_feature_list,
+        min_gene_frequency = 1,
+        annot = pgx$genes,
+        filter_genes = FALSE
+      )
 
-    # merge go.gmt with G
-    G <- playbase::merge_sparse_matrix(
-      m1 = G,
-      m2 = Matrix::t(go.gmt)
-    )
+      # merge go.gmt with G
+      G <- playbase::merge_sparse_matrix(
+        m1 = G,
+        m2 = Matrix::t(go.gmt)
+      )
+    }
   }
 
   # NEW: convert G feature/symbol/human_ortholog to SYMBOL

R/pgx-wgcna.R

@@ -84,7 +84,7 @@ pgx.wgcna <- function(
   nmissing <- sum(is.na(X))
   if (nmissing > 0) {
     message("Found ", nmissing, " missing values in X. Removing prior to WGCNA.")
-    X <- X[complete.cases(X), ]
+    X <- X[complete.cases(X), , drop = FALSE]
   }
   sdx <- matrixStats::rowSds(X, na.rm = TRUE)
   X <- X[sdx > 0.1 * mean(sdx, na.rm = TRUE), ] ## filter low SD