alt cell name smouse

cell_types.R

@@ -0,0 +1,82 @@
+# 13.1 Cell types data set
+# 13.1.1 ST1
+cell_types <- as.matrix(read.delim("omics/all_cell_types.txt", sep =
+                                     "\t", row.names = 1))
+
+
+# 13.1.2 ST2
+cell_types[1:5,1:5]
+dim(cell_types)
+
+
+# 13.1.3 ST3
+colnames(cell_types)
+
+
+# 13.1.4 ST4
+table(cell_types)
+cell_types[,"LTHSC"]
+
+
+# 13.1.5 ST5
+sort(colSums(cell_types)) |> sum()
+
+
+# 13.1.6 ST6
+
+
+
+
+# 13.1.7 ST7
+cell_labels <- sub("_.*", "", rownames(cell_types))
+table(cell_labels)
+# HSPC LT.HSC   Prog 
+# 852    216    852 
+# 701    155    798 orginal
+
+
+# 13.1.8 ST8
+colSums(cell_types[grep("LT.HSC", rownames(cell_types)),])
+colSums(cell_types[grep("HSPC", rownames(cell_types)),])
+colSums(cell_types[grep("Prog", rownames(cell_types)),])
+
+
+# 13.1.9 ST10
+length(colnames(lthsc))
+length(rownames(cell_types))
+length(intersect(colnames(lthsc),rownames(cell_types)))
+# 13.2 Combining the gene expression data with the cell type information
+# Back to questions
+
+
+cell_is_cmp <- clean_cell_types[,"CMP"]==1
+cmp_cell_names <- rownames(clean_cell_types[cell_is_cmp,])
+cmp_expression <- gene_counts[,cmp_cell_names]
+
+
+
+# my code ---------------------------------------------------------
+library(tidyverse)
+# import each of the data sets
+# 🐭 import the data
+hspc <- read_csv("omics/week-5/data-raw/surfaceome_hspc.csv")
+prog <- read_csv("omics/week-5/data-raw/surfaceome_prog.csv")
+
+# what are the name of the cells we have data for
+hspc_cells <- colnames(hspc[-1])
+prog_cells <- colnames(prog[-1])
+all_cells <- c(hspc_cells, prog_cells)
+
+# import the extra cell typ info
+cell_types <- read_table("omics/all_cell_types.txt")
+
+
+# subset the extra cell info using only cells for for we have expression data
+cell_types <- cell_types |> 
+  filter(cell %in% all_cells)
+
+
+# write that to file
+write_csv(cell_types, "omics/er_cell_types.csv")
+
+# 

omics/all_cell_types.txt

@@ -1,4 +1,4 @@
-	LTHSC_broad	LMPP_broad	MPP_broad	CMP_broad	MEP_broad	GMP_broad	MPP1_broad	MPP2_broad	MPP3_broad	STHSC_broad	LTHSC	LMPP	MPP	CMP	MEP	GMP	MPP1	MPP2	MPP3	STHSC	ESLAM	HSC1	Projected
+cell	LTHSC_broad	LMPP_broad	MPP_broad	CMP_broad	MEP_broad	GMP_broad	MPP1_broad	MPP2_broad	MPP3_broad	STHSC_broad	LTHSC	LMPP	MPP	CMP	MEP	GMP	MPP1	MPP2	MPP3	STHSC	ESLAM	HSC1	Projected
 HSPC_001	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
 HSPC_002	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
 HSPC_003	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0