fixes #29

ParkerICI · Jan 16, 2020 · e0324f6 · e0324f6
1 parent 8318423
commit e0324f6
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: premessa
 Type: Package
 Title: R package for pre-processing of flow and mass cytometry data
-Version: 0.2.4
+Version: 0.2.5
 Author: "Pier Federico Gherardini <[email protected]> [aut, cre]"
 Description: This package includes panel editing/renaming for FCS files, bead-based normalization and debarcoding.
 Imports: shiny (>= 0.14), flowCore, reshape, ggplot2, hexbin, gridExtra, rhandsontable, jsonlite

diff --git a/R/fcs_io.R b/R/fcs_io.R
@@ -27,7 +27,7 @@ update_flowFrame_keywords <- function(flowFrame, exprs.m, desc = NULL, data.rang
         keyval[[n]] <- colnames(exprs.m)[i]
 
         if(data.range == "data")
-            keyval[[r]] <- ceiling(max(exprs.m[,i]) - min(exprs.m[,i]))
+            keyval[[r]] <- ceiling(max(exprs.m[,i]))
         else if(is.numeric(data.range))
             keyval[[r]] <- data.range
         else

diff --git a/R/normalize_cytof.R b/R/normalize_cytof.R
@@ -146,7 +146,8 @@ get_mahalanobis_distance_from_beads <- function(m, beads.events, beads.cols.name
     beads.data <- m[beads.events,]
 
     cov.m <- cov(beads.data)
-    ret <- sqrt(mahalanobis(m, colMeans(beads.data), cov.m))
+    ret <- sqrt(mahalanobis(m, colMeans(beads.data), cov.m, tol = 1e-30))
+
     return(ret)
 }