refactor R scripts to run in convert directory of test data (c1f54747) · Commits · github_fork / Universc

sub/MakeGBM_10x_v_convert.R

+4 −3

Original line number	Diff line number	Diff line
		@@ -5,8 +5,9 @@ if(!require(Seurat)){install.packages("Seurat")}


		#####Input files#####
		Cellranger.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_10x/INPUT/cellranger3.0.2/outs/filtered_feature_bc_matrix"
		Convert.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_10x/INPUT/convert1.0.0/outs/filtered_feature_bc_matrix"
		Cellranger.INPUT <- "tiny-count-v3-v302/outs/outs/filtered_feature_bc_matrix"
		Convert.INPUT <- "test-10x-v3-v302/outs/filtered_feature_bc_matrix"
		Out.dir <- "test_10x_GBM"
		##########

		#####Read in input files#####
		@@ -50,7 +51,7 @@ Convert.GBM <- Convert.GBM[order(rownames(Convert.GBM)),]
		##########

		#####Output GBM#####
		Out.dir <- "/Users/kai/Desktop/convert_similarity_test/test_10x/01_GBM"
		system(paste("mkdir -p", Out.dir)
		Cellranger.file <- paste(Out.dir, "cellranger3.0.2_GBM.txt", sep="/")
		Convert.file <- paste(Out.dir, "convert1.0.0_GBM.txt", sep="/")

+4 −3

Original line number	Diff line number	Diff line
		@@ -5,8 +5,9 @@ if(!require(Seurat)){install.packages("Seurat")}


		#####Input files#####
		Nadia.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_Nadia/INPUT/dropseqpipe0.6/samples/SRR1873277_S1_L001/umi"
		Convert.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_Nadia/INPUT/convert1.0.0/outs/filtered_feature_bc_matrix"
		Nadia.INPUT <- "test-dropseqpipe-dev/samples/SRR1873277_S1_L001/umi"
		Convert.INPUT <- "test-dropseq-v302/outs/filtered_feature_bc_matrix"
		Out.dir <- "test_DropSeq_GBM"
		##########

		#####Read in input files#####
		@@ -47,7 +48,7 @@ Convert.GBM <- Convert.GBM[order(rownames(Convert.GBM)),]
		##########

		#####Output GBM#####
		Out.dir <- "/Users/kai/Desktop/convert_test/test_Nadia/01_GBM"
		system(paste("mkdir -p", Out.dir)
		Nadia.file <- paste(Out.dir, "dropseqpipe0.6_GBM.txt", sep="/")
		Convert.file <- paste(Out.dir, "convert1.0.0_GBM.txt", sep="/")

+4 −3

Original line number	Diff line number	Diff line
		@@ -5,8 +5,9 @@ if(!require(Seurat)){install.packages("Seurat")}


		#####Input files#####
		ICELL8.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_ICELL8/INPUT/mappa0.9beta/test-icell8-custom-mappa-0.9_genematrix.csv"
		Convert.INPUT <- "/Users/kai/Desktop/convert_similarity_test/test_ICELL8/INPUT/convert1.0.0/outs/filtered_feature_bc_matrix"
		ICELL8.INPUT <- "test-icell8-custom-mappa-0.9/test-icell8-custom-mappa-0.9_genematrix.csv"
		Convert.INPUT <- "test-icell8-custom-v302/outs/filtered_feature_bc_matrix"
		Out.dir <- "test_ICELL8_GBM"
		##########

		#####Read in input files#####
		@@ -49,7 +50,7 @@ Convert.GBM <- Convert.GBM[order(rownames(Convert.GBM)),]
		##########

		#####Output GBM#####
		Out.dir <- "/Users/kai/Desktop/convert_similarity_test/test_ICELL8/01_GBM"
		system(paste("mkdir -p", Out.dir)
		ICELL8.file <- paste(Out.dir, "mappa0.9beta_GBM.txt", sep="/")
		Convert.file <- paste(Out.dir, "convert1.0.0_GBM.txt", sep="/")