--- a
+++ b/man/get_tcga_exp.Rd
@@ -0,0 +1,58 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/GetTcgaExp.R
+\name{get_tcga_exp}
+\alias{get_tcga_exp}
+\title{TCGA Expression Data Processing}
+\usage{
+get_tcga_exp(
+  counts_file_path,
+  gene_probes_file_path,
+  phenotype_file_path,
+  output_file_path
+)
+}
+\arguments{
+\item{counts_file_path}{File path to the counts data (usually in the form of a large matrix with gene expression data).}
+
+\item{gene_probes_file_path}{File path containing the gene probes data.}
+
+\item{phenotype_file_path}{File path to the phenotype data, which includes various sample attributes.}
+
+\item{output_file_path}{Path where the output files, distinguished between tumor and normal, will be saved.}
+}
+\value{
+A list containing matrices for tumor and normal expression data.
+}
+\description{
+This function processes expression data and phenotype information, separates tumor and normal samples,
+and saves the results into different files. It's specifically designed for data obtained from TCGA.
+}
+\note{
+IMPORTANT: This function assumes that the input files follow a specific format and structure, typically found in TCGA data releases.
+Users should verify their data's compatibility. Additionally, the function does not perform error checking on the data's content,
+which users should handle through proper preprocessing.
+
+CRITICAL: The 'output_file_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, as the function will create further subdivisions in the specified
+path for tumor or normal tissues. Please structure the 'output_file_path' following this pattern: './your_directory/your_sample_type.exp.rds'.
+}
+\examples{
+counts_file <- system.file("extdata", "TCGA-SKCM.htseq_counts_test.tsv", package = "TransProR")
+gene_probes_file <- system.file("extdata",
+                                "TCGA_gencode.v22.annotation.gene.probeMap_test",
+                                package = "TransProR")
+phenotype_file <- system.file("extdata", "TCGA-SKCM.GDC_phenotype_test.tsv", package = "TransProR")
+ouput_file <- file.path(tempdir(), "SKCM_Skin_TCGA_exp_test.rds")
+
+SKCM_exp <- get_tcga_exp(
+  counts_file_path = counts_file,
+  gene_probes_file_path = gene_probes_file,
+  phenotype_file_path = phenotype_file,
+  output_file_path = ouput_file
+)
+head(SKCM_exp[["tumor_tcga_data"]])[1:5, 1:5]
+head(SKCM_exp[["normal_tcga_data"]], n = 10) # Because there is only one column.
+}
+\author{
+Dongyue Yu
+}