Merge pull request #226 from satijalab/fix-runalra

anashen · web-flow · commit 9371845c8d4c · 2026-01-08T10:43:57.000-05:00
Update GetAssayData call in RunALRA.Seurat to use layer param
diff --git a/R/alra.R b/R/alra.R
@@ -200,7 +200,7 @@ RunALRA.Seurat <- function(
     k <- alra.previous[["k"]]
     message("Using previously computed value of k")
   }
-  data.used <- GetAssayData(object = object, assay = assay, slot = slot)[genes.use,]
+  data.used <- GetAssayData(object = object, assay = assay, layer = slot)[genes.use,]
   # Choose k with heuristics if k is not given
   if (is.null(x = k)) {
     # set K based on data dimension

Original file line number	Diff line number	Diff line change
`@@ -200,7 +200,7 @@ RunALRA.Seurat <- function(`
`200`	`200`	`k <- alra.previous[["k"]]`
`201`	`201`	`message("Using previously computed value of k")`
`202`	`202`	`}`
`203`		`- data.used <- GetAssayData(object = object, assay = assay, slot = slot)[genes.use,]`
	`203`	`+ data.used <- GetAssayData(object = object, assay = assay, layer = slot)[genes.use,]`
`204`	`204`	`# Choose k with heuristics if k is not given`
`205`	`205`	`if (is.null(x = k)) {`
`206`	`206`	`# set K based on data dimension`