Anon data code.

dev/anonymise-data.R

@@ -12,20 +12,37 @@ change_gene_id <- function(id) {
 anonymise_data <- function(data) {
     # Create a copy of the original data
     dt_anon <- dt$copy(data)
+    meta_cols <- c("GeneID", "GeneSymbol", "GeneBiotype")
 
     # Change last 3 digits of GeneID
     dt_anon[, GeneID := sapply(GeneID, change_gene_id)]
 
     # Get the names of numeric columns (excluding GeneID, GeneSymbol, and GeneBiotype)
     numeric_cols <- setdiff(
         names(dt_anon)[sapply(dt_anon, is.numeric)], 
-        c("GeneID", "GeneSymbol", "GeneBiotype")
+        meta_cols
     )
 
     # Randomly add 1 or 2 to some cells in numeric columns
     for (col in numeric_cols) {
         dt_anon[, (col) := get(col) + sample(c(0, 1, 2), .N, replace = TRUE, prob = c(0.85, 0.1, 0.05))]
     }
+
+    # rename the columns
+    # select random capital letter from alphabet
+    letter <- sample(LETTERS, 1)
+    # select random number from 0 to 9
+    num <- sample(1:9, 1)
+
+    sample_names <- colnames(dt_anon)
+    sample_names <- sample_names[!sample_names %in% meta_cols]
+
+    # remove the first char from sample names
+    sample_names <- substr(sample_names, 3, nchar(sample_names))
+    # add the random letter and number to the start of the sample names
+    sample_names <- paste0(letter, num, sample_names)
+
+    colnames(dt_anon) <- c(meta_cols, sample_names)
 
     return(dt_anon[])
 }

dev/save-data.R

@@ -3,10 +3,21 @@ box::use(dt = data.table)
 box::use(dev/`anonymise-data`[ anonymise_data ])
 
 # 2. Feature counts genes
-feature_counts0 <- read.csv("dev/data/feature-counts-genes.csv")
+feature_counts0 <- read.csv("dev/data/original.ignore/feature-counts-genes.csv")
 dt$setDT(feature_counts0)
 
+# save original colnames
+sample_names <- colnames(feature_counts0)
+sample_names <- sample_names[!sample_names %in% c("GeneID", "GeneSymbol", "GeneBiotype")]
+sample_names <- dt$data.table(original = sample_names)
+
 feature_counts <- anonymise_data(feature_counts0)
+
+sample_names[, new_name := colnames(feature_counts)[4:ncol(feature_counts)] ]
+
+dt$fwrite(sample_names, "dev/data/original.ignore/new-names-table.csv")
+dt$fwrite(feature_counts, "dev/data/feature-counts-genes.csv")
+
 use_data(feature_counts, overwrite = TRUE)
 
 # 3. Volcano differential expression