--- a/scater-create-qcmetric-ready-sce.R	Tue Sep 03 14:25:32 2019 -0400
+++ b/scater-create-qcmetric-ready-sce.R	Thu Sep 09 12:23:33 2021 +0000
@@ -8,67 +8,60 @@
 
 # parse options
 #SCE-specific options
-option_list = list(
+option_list <- list(
   make_option(
     c("-a", "--counts"),
     action = "store",
     default = NA,
-    type = 'character',
+    type = "character",
     help = "A tab-delimited expression matrix. The first column of all files is assumed to be feature names and the first row is assumed to be sample names."
   ),
   make_option(
     c("-r", "--row-data"),
     action = "store",
     default = NULL,
-    type = 'character',
+    type = "character",
     help = "Path to TSV (tab-delimited) format file describing the features. Row names from the expression matrix (-a), if present, become the row names of the SingleCellExperiment."
   ),
   make_option(
     c("-c", "--col-data"),
     action = "store",
     default = NULL,
-    type = 'character',
+    type = "character",
     help = "Path to TSV format file describing the samples (annotation). The number of rows (samples) must equal the number of columns in the expression matrix."
   ),
   #The scater-specific options
   make_option(
-    c("--assay-name"),
-    action = "store",
-    default = 'counts',
-    type = 'character',
-    help= "String specifying the name of the 'assay' of the 'object' that should be used to define expression."
-  ),
-  make_option(
     c("-f", "--mt-controls"),
     action = "store",
     default = NULL,
-    type = 'character',
+    type = "character",
     help = "Path to file containing a list of the mitochondrial control genes"
   ),
   make_option(
     c("-p", "--ercc-controls"),
     action = "store",
     default = NULL,
-    type = 'character',
+    type = "character",
     help = "Path to file containing a list of the ERCC controls"
   ),
   make_option(
     c("-l", "--cell-controls"),
     action = "store",
     default = NULL,
-    type = 'character',
+    type = "character",
     help = "Path to file (one cell per line) to be used to derive a vector of cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)."
   ),
   make_option(
     c("-o", "--output-loom"),
     action = "store",
     default = NA,
-    type = 'character',
+    type = "character",
     help = "File name in which to store the SingleCellExperiment object in Loom format."
   )
 )
 
-opt <- wsc_parse_args(option_list, mandatory = c('counts', 'output_loom'))
+opt <- wsc_parse_args(option_list, mandatory = c("counts", "output_loom"))
 
 # Read the expression matrix
 
@@ -79,64 +72,61 @@
 
 rowdata <- opt$row_data
 
-if ( ! is.null(opt$row_data) ){
+if (! is.null(opt$row_data)) {
   rowdata <- read.delim(opt$row_data)
 }
 
 coldata <- opt$col_data
 
-if ( ! is.null(opt$col_data) ){
+if (! is.null(opt$col_data)) {
   coldata <- read.delim(opt$col_data)
 }
 
 # Now build the object
-assays <- list(as.matrix(reads))
-names(assays) <- c(opt$assay_name)
-scle <- SingleCellLoomExperiment(assays = assays, colData = coldata, rowData = rowdata)
-# Define spikes (if supplied)
 
-
+sce <- SingleCellLoomExperiment(assays = list(counts = as.matrix(reads)), colData = coldata)
 #Scater options
 
 # Check feature_controls (only mitochondrial and ERCC used for now)
-feature_controls_list = list()
-if (! is.null(opt$mt_controls) && opt$mt_controls != 'NULL'){
-  if (! file.exists(opt$mt_controls)){
-    stop((paste('Supplied feature_controls file', opt$mt_controls, 'does not exist')))
+
+if (! is.null(opt$mt_controls)) {
+  if (! file.exists(opt$mt_controls)) {
+    stop((paste("Supplied feature_controls file", opt$mt_controls, "does not exist")))
   } else {
-    mt_controls <- readLines(opt$mt_controls)
-    feature_controls_list[["MT"]] <- mt_controls
+    mts <- readLines(opt$mt_controls)
   }
+} else {
+  mts <- NULL
 }
 
-if (! is.null(opt$ercc_controls) && opt$ercc_controls != 'NULL'){
-  if (! file.exists(opt$ercc_controls)){
-    stop((paste('Supplied feature_controls file', opt$ercc_controls, 'does not exist')))
+if (! is.null(opt$ercc_controls)) {
+  if (! file.exists(opt$ercc_controls)) {
+    stop((paste("Supplied feature_controls file", opt$ercc_controls, "does not exist")))
   } else {
     ercc_controls <- readLines(opt$ercc_controls)
-    feature_controls_list[["ERCC"]] <- ercc_controls
   }
 } else {
-  ercc_controls <- character()
+  ercc_controls <- NULL
 }
 
 # Check cell_controls
-cell_controls_list <- list()
-if (! is.null(opt$cell_controls) && opt$cell_controls != 'NULL'){
-  if (! file.exists(opt$cell_controls)){
-    stop((paste('Supplied feature_controls file', opt$cell_controls, 'does not exist')))
+
+if (! is.null(opt$cell_controls)) {
+  if (! file.exists(opt$cell_controls)) {
+    stop((paste("Supplied feature_controls file", opt$cell_controls, "does not exist")))
   } else {
     cell_controls <- readLines(opt$cell_controls)
-    cell_controls_list[["empty"]] <- cell_controls
   }
+} else {
+  cell_controls <- NULL
 }
 
+# calculate QCMs
 
-# calculate QCMs
-scle  <- calculateQCMetrics(scle, exprs_values = opt$assay_name, feature_controls = feature_controls_list, cell_controls = cell_controls_list)
+sce <- addPerCellQC(sce, subsets = list(Mito = mts, ERCC = ercc_controls, cell_controls = cell_controls))
 
 # Output to a Loom file
 if (file.exists(opt$output_loom)) {
   file.remove(opt$output_loom)
 }
-export(scle, opt$output_loom, format='loom')
+export(sce, opt$output_loom, format = "loom")