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Preprocess TCGA RNA-seq Data

Source: R/tcga_rna_preps.R
tcga_rna_preps.Rd

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

Dongqiang Zeng

Examples

eset_stad <- load_data("eset_stad")
eset <- tcga_rna_preps(
  eset = eset_stad, id_type = "ensembl", input_type = "count",
  output = "tumor", output_type = "tpm", annotation = TRUE
)
#> ℹ Sample type distribution:
#> 
#>    
#> 10 
#> ℹ Adjacent normal samples removed
#> ℹ TCGA barcode reduced to 12 digits
#> ℹ Duplicate barcode check:
#>    Mode   FALSE 
#> logical      10 
#> ℹ Converting count to TPM
#> ℹ Using local annotation (anno_grch38) for TPM conversion
#> ! Omitting 3985 genes without length information
#> Warning: longer object length is not a multiple of shorter object length
#> ℹ No duplicate gene symbols found.