Use rowData(altExp(x)) for spike concs, work towards #175 and #169

catavallejos · Sep 9, 2020 · 0d7558c · 0d7558c
1 parent 517aad3
commit 0d7558c
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Showing 2 changed files with 11 additions and 19 deletions.
diff --git a/R/newBASiCS_Data.R b/R/newBASiCS_Data.R
@@ -76,7 +76,7 @@ newBASiCS_Data <- function(Counts,
                            SpikeInfo = NULL,
                            BatchInfo = NULL,
                            SpikeType = "ERCC") {
-
+  .Deprecated()
   if (!inherits(Counts, "matrix")) {
     stop("Counts must be a matrix.")
   }
@@ -115,19 +115,19 @@ newBASiCS_Data <- function(Counts,
       )
     }
     # Extracting spike-in input molecules in the correct order
-    if (sum(!(GeneName[Tech] %in% SpikeInfo[, 1])) > 0) {
+    if (any(!(GeneName[Tech] %in% SpikeInfo[, 1]))) {
       stop("'SpikeInfo' is missing information for some of the spikes")
     }
-    if (sum(!(SpikeInfo[, 1] %in% GeneName[Tech])) > 0) {
+    if (any(!(SpikeInfo[, 1] %in% GeneName[Tech]))) {
       stop("'SpikeInfo' includes spikes that are not in 'Counts'")
     }
     if (any(GeneName[Tech] != SpikeInfo[, 1])) {
       # Re-order spike-ins in SpikeInfo if required
       matching <- match(GeneName[Tech], SpikeInfo[, 1])
       SpikeInfo <- SpikeInfo[matching, ]
     }
-    metadata(Data)$SpikeInput <- SpikeInfo
-    altExp(Data, "spike-ins") <- SummarizedExperiment(CountsTech)
+    altExp(Data, "spike-ins") <- SummarizedExperiment(CountsTech, 
+      rowData = SpikeInfo)
     WithSpikes <- TRUE
   } else {
     message("The data does not contain spike-in genes")

diff --git a/R/utils_Data.R b/R/utils_Data.R
@@ -49,23 +49,15 @@
         errors <- c(errors, "spike-in counts must be provided as 'altExp'. \n")
       }
     } else {
-      if (!("SpikeInput" %in% names(metadata(Data)))) {
-        errors <- c(errors, "'SpikeInput' was not provided as metadata.\n")
+      if (is.null(colnames(rowData(altExp(Data))))) {
+        errors <- c(errors, "rowData of altExp is missing!\n")
       }
       # Extract spike-ins
       CountsTech <- assay(altExp(Data))
-      SpikeInput <- metadata(Data)$SpikeInput
+      SpikeInput <- rowData(altExp(Data))
       # Validity checks for SpikeInput
-      if (!is.data.frame(SpikeInput)) {
-        errors <- c(errors, "'SpikeInput' must be a 'data.frame'.\n")
-      }
       if (ncol(SpikeInput) != 2) {
-        errors <- c(errors, "'SpikeInput' must have two columns only.\n")
-      }
-      if (nrow(SpikeInput) != nrow(CountsTech)) {
-        errors <- c(errors,
-          "'SpikeInput' dimensions not compatible with 'altExp'. \n"
-        )
+        errors <- c(errors, "rowData of altExp must have two columns only.\n")
       }
       # Validity checks for input concentrations
       if (!(is.numeric(SpikeInput[, 2]) & all(SpikeInput[, 2] > 0) & 
@@ -79,14 +71,14 @@
         errors <- c(errors, "'SpikeInput' row order does not match 'altExp'.\n")
       }
       # Check all cells have non-zero total count
-      if (sum(Matrix::colSums(CountsTech) == 0) > 0) {
+      if (any(Matrix::colSums(CountsTech) == 0)) {
         errors <- c(errors,
           "Some cells have zero reads mapping back to the 
           spike-in genes. Please remove these before running the MCMC.\n"
         )
       }
       # Check all genes have non-zero total count
-      if (sum(Matrix::rowSums(CountsTech) == 0) > 0) {
+      if (any(Matrix::rowSums(CountsTech) == 0)) {
         errors <- c(errors,
           "Some spike-in genes have zero total reads
           across all cells. Please remove these before running the MCMC.\n"