--- a
+++ b/R/CombatTumor.R
@@ -0,0 +1,100 @@
+#' Process and Correct Batch Effects in Tumor Data
+#'
+#' This function takes a tumor data set, asks the user for specific tumor types to retain,
+#' and then corrects for batch effects using the ComBat_seq function from the 'sva' package.
+#'
+#' @description
+#' The function first extracts histological types from the provided tumor data set.
+#' After displaying these types, the user is prompted to input specific types to retain.
+#' The data is then filtered based on this input.
+#'
+#' Note: This example assumes that different tumor types represent different batches in a general sense.
+#' Users need to adjust the batch and group vectors based on real-life scenarios.
+#'
+#' @param tumor_data_path The path to the tumor data stored in an RDS file.
+#' @param CombatTumor_output_path A character string specifying the path where the output RDS file will be saved.
+#' @param auto_mode Logical. If set to TRUE, the function will not prompt the user for input and
+#'                  will instead use the values provided in default_input. Default is FALSE.
+#' @param default_input Character string. When auto_mode is TRUE, this parameter specifies the default
+#'                      tumor types to be retained. It should be provided as a comma-separated string (e.g., "01,06").
+#'
+#' @return A data.frame with corrected values after the ComBat_seq adjustment. Note that this function also saves the
+#'         combat_count_df data as an RDS file at the specified output path.
+#'
+#' @details
+#' The ComBat_seq function from the sva package is used to correct batch effects.
+#' The function requires the 'sva' package to be installed and loaded externally.
+#'
+#' @examples
+#' tumor_file <- system.file("extdata",
+#'                           "SKCM_Skin_TCGA_exp_tumor_test.rds",
+#'                           package = "TransProR")
+#' output_file <- file.path(tempdir(), "SKCM_combat_count.rds")
+#'
+#'   SKCM_combat_count <- combat_tumor(
+#'   tumor_data_path = tumor_file,
+#'   CombatTumor_output_path = output_file,
+#'   auto_mode = TRUE,
+#'   default_input = "01,06"
+#' )
+#'
+#' head(SKCM_combat_count)[1:5, 1:5]
+#'
+#' @seealso \code{\link[sva]{ComBat_seq}}
+#' @importFrom sva ComBat_seq
+#' @export
+combat_tumor <- function(tumor_data_path, CombatTumor_output_path, auto_mode = FALSE, default_input = "01,06") {
+
+  # Load the tumor data
+  tumor_data <- readRDS(tumor_data_path)
+
+  # Extract histological types
+  TumorHistologicalTypes <- substring(colnames(tumor_data), 14, 15)
+  tumor_hist_table <- table(TumorHistologicalTypes)
+
+  # Display the table to the user
+  message(" ")
+  message("TumorHistologicalTypes:")
+  message(paste(names(tumor_hist_table), tumor_hist_table, sep = ": ", collapse = "\n"))
+  # Add a space after the output for separation
+  message(" ")
+
+  # Ask the user for input or use default input in auto_mode
+  if(auto_mode) {
+    selected_types <- strsplit(default_input, ",")[[1]]
+  } else {
+    message("Please input the tumor types you wish to retain, separated by commas (e.g., 01,06): ")
+    selected_types <- strsplit(readline(), ",")[[1]]
+  }
+
+  # Filter the tumor data based on user's input
+  tumor <- tumor_data[, TumorHistologicalTypes %in% selected_types]
+
+  # Modify the tumor values
+  tumor1 <- 2^(tumor) - 1
+  tumor1 <- apply(tumor1, 2, as.integer)
+  rownames(tumor1) <- rownames(tumor)
+
+  # If only one sample type is chosen, skip batch correction and return modified tumor data
+  if(length(selected_types) == 1) {
+    combat_count_df <- as.data.frame(tumor1)
+  } else {
+    # Create group vector
+    selected_group = rep("all_group", length(which(TumorHistologicalTypes %in% selected_types)))
+
+    # Create batch vector based on group vector
+    selected_batch = match(TumorHistologicalTypes[TumorHistologicalTypes %in% selected_types], selected_types)
+
+    # Correct for batch effects using ComBat_seq
+    combat_count <- sva::ComBat_seq(as.matrix(tumor1),
+                                    batch = selected_batch,
+                                    group = selected_group)
+
+    # Convert matrix to data frame
+    combat_count_df <- as.data.frame(combat_count)
+  }
+
+  saveRDS(combat_count_df, file = CombatTumor_output_path)
+
+  return(combat_count_df)
+}