--- a
+++ b/bin/archr_gene_activity.R
@@ -0,0 +1,48 @@
+# Code for running ArchR to get ene expression matrices out
+# Useful links:
+# https://www.archrproject.com/articles/Articles/tutorial.html
+# https://www.archrproject.com/bookdown/calculating-gene-scores-in-archr.html
+library(optparse)
+
+
+# https://www.r-bloggers.com/passing-arguments-to-an-r-script-from-command-lines/
+# https://stackoverflow.com/questions/13790610/passing-multiple-arguments-via-command-line-in-r
+option_list = list(
+  make_option(c("-f", "--files"), type="character", default=NULL, 
+              help="Comma separated list of files", metavar="character"),
+  make_option(c("-n", "--names"), type="character", default=NULL,
+              help="Comma separated list of names", metavar="character"),
+  make_option(c("-o", "--out"), type="character", default="archr_gene_act", 
+              help="output file name prefix [default= %default]", metavar = "character"),
+  make_option(c("-g", "--genome"), type="character", default="hg38",
+              help="Genome to use [default=%default]", metavar = "character")
+); 
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if (is.null(opt$files)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (input file).n", call.=FALSE)
+}
+
+library(ArchR)
+
+addArchRGenome(opt$genome)
+
+inputFiles = strsplit(opt$files, ",")[[1]]
+inputSampleNames = strsplit(opt$names, ",")[[1]]
+
+ArrowFiles <- createArrowFiles(inputFiles = inputFiles, sampleNames = inputSampleNames, filterTSS = 4, filterFrags = 1000, addTileMat = TRUE, addGeneScoreMat = TRUE)
+proj <- ArchRProject(ArrowFiles = ArrowFiles, outputDirectory = opt$out, copyArrows = TRUE)
+proj <- addIterativeLSI(ArchRProj = proj, useMatrix = "TileMatrix", name = "IterativeLSI")
+proj <- addClusters(input = proj, reducedDims = "IterativeLSI")
+
+# # https://www.bioconductor.org/help/course-materials/2019/BSS2019/04_Practical_CoreApproachesInBioconductor.html
+mat = getMatrixFromProject(proj)
+writeMM(assays(mat)[['GeneScoreMatrix']], paste(opt$out, "_gene_activity.mtx", sep=""))  # Write the numerical matrix
+write.csv(rowData(mat), paste(opt$out, "_gene_activity_var.csv", sep=""))
+write.csv(colData(mat), paste(opt$out, "_gene_activity_obs.csv", sep=""))
+
+# Save the ArchR project
+proj <- saveArchRProject(ArchRProj = proj)