tcga_rna_preps: Preprocess TCGA RNA-seq Data

In IOBR: Immune Oncology Biological Research

Preprocess TCGA RNA-seq Data

Description

Preprocesses TCGA RNA-seq data by modifying sample types, transforming data, and annotating genes based on specified parameters.

Usage

tcga_rna_preps(
  eset,
  id_type = c("ensembl", "symbol"),
  input_type = c("log2count", "count"),
  output = c("tumor", "tumor_normal"),
  output_type = c("tpm", "log2tpm", "count"),
  annotation = TRUE
)

Arguments

eset	Matrix or data frame. RNA-seq gene expression matrix from TCGA.
id_type	Character. Gene identifier type: "ensembl" or "symbol". Default is "ensembl".
input_type	Character. Input data type: "log2count" or "count". Default is "log2count".
output	Character. Sample type: "tumor" or "tumor_normal". Default is "tumor".
output_type	Character. Output data type: "tpm", "log2tpm", or "count". Default is "tpm".
annotation	Logical. Whether to perform gene annotation. Default is TRUE.

Value

Preprocessed gene expression matrix.

Author(s)

Dongqiang Zeng

Examples

# Simulate TCGA-style data with Ensembl IDs
set.seed(123)
sim_eset <- matrix(
  abs(rnorm(500)),
  nrow = 100,
  ncol = 5,
  dimnames = list(
    paste0("ENSG00000", 101:200),
    paste0("TCGA-AB-123", 4:8, "-01A")
  )
)
# Process tumor samples only (output as count for offline testing)
eset <- tcga_rna_preps(
  eset = sim_eset, id_type = "ensembl", input_type = "count",
  output = "tumor", output_type = "count", annotation = FALSE
)
print(dim(eset))

IOBR documentation built on May 30, 2026, 5:07 p.m.