Added file extraction

drieslab · Aug 5, 2024 · c156509 · c156509
1 parent 61629c2
commit c156509
Showing 1 changed file with 18 additions and 1 deletion.
diff --git a/03_session1.Rmd b/03_session1.Rmd
@@ -29,7 +29,7 @@ Visium by 10x Genomics is a spatial gene expression platform that allows for the
 You need to download the expression matrix and spatial information by running these commands:
 
 ```{r, eval=FALSE}
-data_dir <- "data/3_session1"
+data_dir <- "data/03_session1"
 
 dir.create(file.path(data_dir, "Visium_FFPE_Human_Prostate_Cancer"), 
            showWarnings = TRUE, recursive = TRUE)
@@ -54,6 +54,23 @@ download.file(url = "https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium
               destfile = file.path(data_dir, "Visium_FFPE_Human_Normal_Prostate/Visium_FFPE_Human_Normal_Prostate_raw_feature_bc_matrix.tar.gz"))
 ```
 
+## Extracting the downloaded files
+```{r, eval=FALSE}
+
+# The adenocarcinoma sample
+untar(tarfile = file.path(data_dir, "Visium_FFPE_Human_Prostate_Cancer/Visium_FFPE_Human_Prostate_Cancer_spatial.tar.gz"), 
+      exdir = file.path(data_dir, "Visium_FFPE_Human_Prostate_Cancer"))
+
+untar(tarfile = file.path(data_dir, "Visium_FFPE_Human_Prostate_Cancer/Visium_FFPE_Human_Prostate_Cancer_raw_feature_bc_matrix.tar.gz"), 
+      exdir = file.path(data_dir, "Visium_FFPE_Human_Prostate_Cancer"))
+
+# The normal prostate sample
+untar(tarfile = file.path(data_dir, "Visium_FFPE_Human_Normal_Prostate/Visium_FFPE_Human_Normal_Prostate_spatial.tar.gz"), 
+      exdir = file.path(data_dir, "Visium_FFPE_Human_Normal_Prostate"))
+
+untar(tarfile = file.path(data_dir, "Visium_FFPE_Human_Normal_Prostate/Visium_FFPE_Human_Normal_Prostate_raw_feature_bc_matrix.tar.gz"), 
+      exdir = file.path(data_dir, "Visium_FFPE_Human_Normal_Prostate"))
+```
 
 ### Create giotto instructions