--- a
+++ b/man/combat_tumor.Rd
@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CombatTumor.R
+\name{combat_tumor}
+\alias{combat_tumor}
+\title{Process and Correct Batch Effects in Tumor Data}
+\usage{
+combat_tumor(
+  tumor_data_path,
+  CombatTumor_output_path,
+  auto_mode = FALSE,
+  default_input = "01,06"
+)
+}
+\arguments{
+\item{tumor_data_path}{The path to the tumor data stored in an RDS file.}
+
+\item{CombatTumor_output_path}{A character string specifying the path where the output RDS file will be saved.}
+
+\item{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.}
+
+\item{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").}
+}
+\value{
+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.
+}
+\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.
+}
+\details{
+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.
+
+
+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}}
+}