Allow NA values for scGateConsensus

bbimber · bbimber · commit 48c4caff1281 · 2024-03-30T19:34:52.000-07:00
diff --git a/singlecell/resources/chunks/CheckExpectations.R b/singlecell/resources/chunks/CheckExpectations.R
@@ -1,4 +1,4 @@
-CheckField <- function(seuratObj, datasetId, fieldName) {
+CheckField <- function(seuratObj, datasetId, fieldName, errorOnNA= TRUE) {
   if (!fieldName %in% names(seuratObj@meta.data)) {
     addErrorMessage(paste0(paste0('Missing ', fieldName, ' for dataset: ', datasetId)))
   }
@@ -47,7 +47,7 @@ for (datasetId in names(seuratObjects)) {
   }
 
   if (requireScGate) {
-    CheckField(seuratObj, datasetId, 'scGateConsensus')
+    CheckField(seuratObj, datasetId, 'scGateConsensus', errorOnNA = FALSE)
   }
 
   if (requireRiraImmune) {

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-CheckField <- function(seuratObj, datasetId, fieldName) {`
	`1`	`+CheckField <- function(seuratObj, datasetId, fieldName, errorOnNA= TRUE) {`
`2`	`2`	`if (!fieldName %in% names(seuratObj@meta.data)) {`
`3`	`3`	`addErrorMessage(paste0(paste0('Missing ', fieldName, ' for dataset: ', datasetId)))`
`4`	`4`	`}`
`@@ -47,7 +47,7 @@ for (datasetId in names(seuratObjects)) {`
`47`	`47`	`}`
`48`	`48`
`49`	`49`	`if (requireScGate) {`
`50`		`- CheckField(seuratObj, datasetId, 'scGateConsensus')`
	`50`	`+ CheckField(seuratObj, datasetId, 'scGateConsensus', errorOnNA = FALSE)`
`51`	`51`	`}`
`52`	`52`
`53`	`53`	`if (requireRiraImmune) {`