Fixed bug where viper and singscore would not run successfully when t…

…here was only one custom gene set and the elements in the gene set were duplicated. Here we thank Zedan Zhang for coming up with the bug.
chuiqin · May 17, 2023 · 5fb5e36 · 5fb5e36
1 parent a205959
commit 5fb5e36
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Showing 2 changed files with 33 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: irGSEA
 Type: Package
 Title: The integration of single cell rank-based gene set enrichment analysis
-Version: 2.1.4
+Version: 2.1.5
 Author: Chuiqin Fan
 Author@R: person("Chuiqin", "Fan", role = c('aut', 'cre'), email = '[email protected]')
 Maintainer: Chuiqin Fan <[email protected]>

diff --git a/R/irGSEA.score.R b/R/irGSEA.score.R
@@ -328,6 +328,10 @@ irGSEA.score <- function(object = NULL, assay = NULL, slot = "data",
     }
 
     h.gsets.list <- geneset %>% purrr::compact()
+
+    # remove duplication
+    h.gsets.list <- lapply(h.gsets.list, function(x){unique(unlist(x))})
+
     # Filter gene sets by minGSSize and maxGSSize
     h.gsets.list2 <- sapply(h.gsets.list, function(x){
       length(x) >= minGSSize & length(x) <= maxGSSize
@@ -1011,13 +1015,34 @@ irGSEA.score <- function(object = NULL, assay = NULL, slot = "data",
 
       viper.scores.list <- list()
       for (k in seq_along(my.matrix.list)) {
-        viper.scores.list[[k]] <- decoupleR::run_viper(mat = as.matrix(my.matrix[, my.matrix.list[[k]]]),
-                                                       net = net,
-                                                       .source='source',
-                                                       .target='target',
-                                                       .mor='weight',
-                                                       minsize = minGSSize,
-                                                       cores = ncores)
+
+        if (length(unique(net$source)) == 1) {
+          net.copy <- rbind(net, net)
+          net.star <- (0.5 * nrow(net.copy))+1
+          net.end <- nrow(net.copy)
+          net.copy$source[net.star:net.end] <- paste0(net$source[1:nrow(net)], "_copy")
+          viper.scores.list[[k]] <- decoupleR::run_viper(mat = as.matrix(my.matrix[, my.matrix.list[[k]]]),
+                                                         net = net.copy,
+                                                         .source='source',
+                                                         .target='target',
+                                                         .mor='weight',
+                                                         minsize = minGSSize,
+                                                         cores = ncores)
+          source <- NULL
+          viper.scores.list[[k]] <- viper.scores.list[[k]] %>%
+            dplyr::filter(source != unique(paste0(net$source[1:nrow(net)], "_copy")))
+
+        }else{
+          viper.scores.list[[k]] <- decoupleR::run_viper(mat = as.matrix(my.matrix[, my.matrix.list[[k]]]),
+                                                         net = net,
+                                                         .source='source',
+                                                         .target='target',
+                                                         .mor='weight',
+                                                         minsize = minGSSize,
+                                                         cores = ncores)
+        }
+
+
         source <- NULL
         condition <- NULL
         score <- NULL