--- a
+++ b/man/Combat_Normal.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CombatNormal.R
+\name{Combat_Normal}
+\alias{Combat_Normal}
+\title{Process and Correct Batch Effects in TCGA's normal tissue and GTEX Data}
+\usage{
+Combat_Normal(
+  TCGA_normal_data_path,
+  gtex_data_path,
+  CombatNormal_output_path,
+  auto_mode = FALSE,
+  default_input = "11,12"
+)
+}
+\arguments{
+\item{TCGA_normal_data_path}{The path to the tumor data stored in an RDS file.}
+
+\item{gtex_data_path}{The path to the GTEX data stored in an RDS file.}
+
+\item{CombatNormal_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
+TGCA's normal tissue types to be retained. It should be provided as a comma-separated string (e.g., "11,12").}
+}
+\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 TCGA's normal tissue 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.
+The GTEX and TCGA's normal tissue datasets are then combined and batch corrected.
+
+Note: This function assumes that TCGA's normal samples and GTEX samples represent different batches.
+}
+\details{
+This function takes a TCGA's normal tissue data set and a pre-saved GTEX data set, asks the user
+for specific TCGA's normal tissue types to retain, then merges the two datasets. The merged dataset
+is then corrected 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.
+
+The example code uses `tempfile()` to generate temporary paths dynamically during execution.
+These paths are valid during the `R CMD check` process, even if no actual files exist,
+because `tempfile()` generates a unique file path that does not depend on the user's file system.
+Using `tempfile()` ensures that the example code does not rely on specific external files and
+avoids errors during `R CMD check`. CRAN review checks for documentation correctness
+and syntax parsing, not the existence of actual files, as long as the example code is syntactically valid.
+}
+\examples{
+TCGA_normal_file <- system.file("extdata",
+                                "SKCM_Skin_TCGA_exp_normal_test.rds",
+                                package = "TransProR")
+gtex_file <- system.file("extdata", "Skin_SKCM_Gtex_test.rds", package = "TransProR")
+output_file <- file.path(tempdir(), "SKCM_Skin_Combat_Normal_TCGA_GTEX_count.rds")
+
+SKCM_Skin_Combat_Normal_TCGA_GTEX_count <- Combat_Normal(
+  TCGA_normal_data_path = TCGA_normal_file,
+  gtex_data_path = gtex_file,
+  CombatNormal_output_path = output_file,
+  auto_mode = TRUE,
+  default_input = "skip"
+)
+head(SKCM_Skin_Combat_Normal_TCGA_GTEX_count)[1:5, 1:5]
+
+}
+\seealso{
+\code{\link[sva]{ComBat_seq}}
+}