From 600188a2a897c569374327a1ef19e5e61e7f8097 Mon Sep 17 00:00:00 2001
From: Sidhant Puntambekar <sidhantnp@yahoo.com>
Date: Tue, 14 Jul 2020 11:31:56 -0600
Subject: [PATCH] Added R file for GSE146771 ref matrix

---
 R/homoSapiens/GSE146771/GSE146771.r | 33 +++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 R/homoSapiens/GSE146771/GSE146771.r

diff --git a/R/homoSapiens/GSE146771/GSE146771.r b/R/homoSapiens/GSE146771/GSE146771.r
new file mode 100644
index 0000000..86c47d7
--- /dev/null
+++ b/R/homoSapiens/GSE146771/GSE146771.r
@@ -0,0 +1,33 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+
+mat_Leukocyte <- read_tsv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146771/suppl/GSE146771_CRC.Leukocyte.10x.TPM.txt.gz")
+mat_Leukocyte <- mat_Leukocyte %>%
+  # as.data.frame() %>%
+  column_to_rownames('gene')
+#  as.matrix() %>%
+#  t()
+mat_Leukocyte[1:5, 1:5]
+
+meta_Leukocyte <- read_tsv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146771/suppl/GSE146771_CRC.Leukocyte.10x.Metadata.txt.gz")
+meta_Leukocyte
+sum(colnames(mat_Leukocyte) %in% meta_Leukocyte$cluster)
+ncol(mat_Leukocyte)
+
+source("~/Reference-Matrix-Generation/R/utils/check.r")
+checkRawCounts(as.matrix(mat_Leukocyte))
+
+new_ref_matrix <- average_clusters(mat = mat_Leukocyte, metadata = meta_Leukocyte, if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_Leukocyte, metadata = meta_Leukocyte, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE146771Hashed.rds")
+saveRDS(new_ref_matrix, "GSE146771.rds")
\ No newline at end of file