--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-pca-filter.R	Tue Sep 03 14:30:21 2019 -0400
@@ -0,0 +1,60 @@
+#!/usr/bin/env Rscript
+#Filters a SingleCellExperiment object, using PCA on the following metrics:
+# "pct_counts_top_100_features"
+# "total_features"
+# "pct_counts_feature_control"
+# "total_features_feature_control"
+# "log10_total_counts_endogenous"
+# "log10_total_counts_feature_control"
+
+# Load optparse we need to check inputs
+library(optparse)
+library(workflowscriptscommon)
+library(LoomExperiment)
+library(scater)
+library(mvoutlier)
+
+# parse options
+option_list = list(
+  make_option(
+    c("-i", "--input-loom"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "A SingleCellExperiment object file in Loom format."
+  ),
+  make_option(
+    c("-o", "--output-loom"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "File name in which to store the SingleCellExperiment object in Loom format."
+  )
+)
+
+opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_loom'))
+
+# Check parameter values
+
+if ( ! file.exists(opt$input_loom)){
+  stop((paste('File', opt$input_loom, 'does not exist')))
+}
+
+# Input from Loom format
+
+scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
+print(paste("Starting with", ncol(scle), "cells and", nrow(scle), "features."))
+
+# Run PCA on data and detect outliers
+scle <- runPCA(scle, use_coldata = TRUE, detect_outliers = TRUE)
+
+# Filter out outliers
+scle <- scle[, !scle$outlier]
+
+print(paste("Ending with", ncol(scle), "cells and", nrow(scle), "features."))
+
+# Output to a Loom file
+if (file.exists(opt$output_loom)) {
+  file.remove(opt$output_loom)
+}
+export(scle, opt$output_loom, format='loom')