Bug fix - errors on genes with 0 variance under certain normalization schemes.

deto · deto · commit dbe93b543598 · 2020-02-14T12:36:05.000-08:00
diff --git a/R/NormalizationMethods.R b/R/NormalizationMethods.R
@@ -110,17 +110,20 @@ getNormalizedCopySparse <- function(data, func) {
     if (func == "znorm_rows" || func == "znorm_rows_then_columns") {
         rowOffsets <- rowMeans(data) * -1
         rowScaleFactors <- rowVarsSp(data) ** -0.5
+        rowScaleFactors[is.infinite(rowScaleFactors)] <- 1
     }
 
     if (func == "znorm_columns") {
         colOffsets <- colMeans(data) * -1
         colScaleFactors <- colVarsSp(data) ** -0.5
+        colScaleFactors[is.infinite(colScaleFactors)] <- 1
     }
 
     if (func == "znorm_rows_then_columns") {
         result <- .colNormHelper(data, rowOffsets, rowScaleFactors)
         colOffsets <- result$colOffsets
         colScaleFactors <- result$colScaleFactors
+        colScaleFactors[is.infinite(colScaleFactors)] <- 1
     }
 
     nd <- NormData(data, rowOffsets = rowOffsets, colOffsets = colOffsets,

Original file line number	Diff line number	Diff line change
`@@ -110,17 +110,20 @@ getNormalizedCopySparse <- function(data, func) {`
`110`	`110`	`if (func == "znorm_rows" \|\| func == "znorm_rows_then_columns") {`
`111`	`111`	`rowOffsets <- rowMeans(data) * -1`
`112`	`112`	`rowScaleFactors <- rowVarsSp(data) ** -0.5`
	`113`	`+ rowScaleFactors[is.infinite(rowScaleFactors)] <- 1`
`113`	`114`	`}`
`114`	`115`
`115`	`116`	`if (func == "znorm_columns") {`
`116`	`117`	`colOffsets <- colMeans(data) * -1`
`117`	`118`	`colScaleFactors <- colVarsSp(data) ** -0.5`
	`119`	`+ colScaleFactors[is.infinite(colScaleFactors)] <- 1`
`118`	`120`	`}`
`119`	`121`
`120`	`122`	`if (func == "znorm_rows_then_columns") {`
`121`	`123`	`result <- .colNormHelper(data, rowOffsets, rowScaleFactors)`
`122`	`124`	`colOffsets <- result$colOffsets`
`123`	`125`	`colScaleFactors <- result$colScaleFactors`
	`126`	`+ colScaleFactors[is.infinite(colScaleFactors)] <- 1`
`124`	`127`	`}`
`125`	`128`
`126`	`129`	`nd <- NormData(data, rowOffsets = rowOffsets, colOffsets = colOffsets,`