scripts: Add input and analysis script

scripts/input.R

@@ -0,0 +1,38 @@
+# This script reads data from GTEx and transforms it into various formats for
+# further analysis. Note that this requires very good computational resources
+# and especially a lot of RAM because of the size of the data.
+
+library(data.table)
+library(here)
+
+i_am("scripts/input.R")
+
+# Source: https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/
+# GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz
+# The file has been edited removing the lines above the column headers.
+data_wide_samples <- fread(here("scripts", "input", "gtex.tsv.gz"))
+
+setnames(
+  data_wide_samples,
+  c("Name", "Description"),
+  c("gene", "hgnc_symbol")
+)
+
+data_long <- melt(
+  data_wide_samples,
+  id.vars = c("gene", "hgnc_symbol"),
+  variable.name = "sample",
+  value.name = "expression",
+  variable.factor = FALSE
+)
+
+fwrite(
+  data_wide_samples,
+  file = here(
+    "scripts",
+    "input",
+    "data_wide_samples.csv"
+  )
+)
+
+fwrite(data_long, file = here("scripts", "input", "data_long.csv"))