--- a
+++ b/man/merge_gtex_tcga.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MergeGtexTcga.R
+\name{merge_gtex_tcga}
+\alias{merge_gtex_tcga}
+\title{Merge gene expression data from GTEx and TCGA datasets}
+\usage{
+merge_gtex_tcga(
+  gtex_data_path,
+  tcga_exp_path,
+  output_path = "./merged_gtex_tcga_data.rds"
+)
+}
+\arguments{
+\item{gtex_data_path}{A string that specifies the file path to the GTEx data saved in RDS format.}
+
+\item{tcga_exp_path}{A string that specifies the file path to the TCGA expression data saved in RDS format.
+This should be a data.frame with rows as genes and columns as samples.}
+
+\item{output_path}{A string that specifies the path where the merged dataset should be saved.
+The file is saved in '.rds' format. The default path is "./merged_gtex_tcga_data.rds".}
+}
+\value{
+A data frame where rows represent genes and columns represent samples.
+        The data frame contains expression values from both GTEx and TCGA datasets.
+        It saves the merged dataset to the path specified by 'output_path'.
+}
+\description{
+This function merges gene expression data obtained from the GTEx (Genotype-Tissue Expression) and TCGA (The Cancer Genome Atlas) datasets.
+It is assumed that both datasets are in '.rds' format and have genes as row names. The merged dataset is saved as an RDS file at the specified output path.
+}
+\details{
+It is assumed that both datasets are in '.rds' format and have genes as row names.
+}
+\note{
+CRITICAL: The 'output_path' parameter must end with '.rds' to be properly recognized by the function. It is also highly recommended
+      that the path includes specific identifiers related to the target samples. Please structure the 'output_path' following this pattern: './your_directory/merged.your_sample_type.gtex.tcga.data.rds'.
+}
+\examples{
+tumor_file <- system.file("extdata",
+                          "removebatch_SKCM_Skin_TCGA_exp_tumor_test.rds",
+                          package = "TransProR")
+Normal_file <- system.file("extdata",
+                           "removebatch_SKCM_Skin_Normal_TCGA_GTEX_count_test.rds",
+                           package = "TransProR")
+ouput_file <- file.path(tempdir(), "all_data.rds")
+
+all_data <- merge_gtex_tcga(gtex_data_path = tumor_file,
+                            tcga_exp_path = Normal_file,
+                            output_path = ouput_file)
+
+}