Debug nimble data issue

bimberlabinternal · Jan 28, 2025 · 17142f7 · 17142f7
1 parent f6e602f
commit 17142f7
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diff --git a/R/NimbleAPI.R b/R/NimbleAPI.R
@@ -220,6 +220,11 @@ DownloadAndAppendNimble <- function(seuratObject, targetAssayName, outPath=tempd
         }
       }
 
+      d <- as.integer(nimbleTable$V2)
+      if (any(is.na(d))){
+        stop(paste0('Non-integer count values found, were: ', paste0(head(unique(df$nimbleTable[is.na(d)])), collapse = ',')))
+      }
+
       # strip hyphens
       nimbleTable$V3 <- gsub(nimbleTable$V3, pattern = '-[0-9]$', replacement = '')
 

diff --git a/R/NimbleAppend.R b/R/NimbleAppend.R
@@ -54,6 +54,11 @@ AppendNimbleCounts <- function(seuratObject, nimbleFile, targetAssayName, maxAmb
     stop("The nimble data contains features with trailing commas. This should not occur.")
   }
 
+  d <- as.integer(df$V2)
+  if (any(is.na(d))){
+    stop(paste0('Non-integer count values found, were: ', paste0(head(df$V2[is.na(d)]), collapse = ',')))
+  }
+
   #Remove ambiguous features
   totalHitsByRow <- sapply(df$V1, function(y){
     return(length(unlist(strsplit(y, split = ','))))