initialize_RNAseq_data: Read all RNA-seq related datasets from TCGA and GTEx

In a3609640/eIF4F.analysis: A R package to analyze eIF4F subunits in human cancers

Read all RNA-seq related datasets from TCGA and GTEx

Description

A wrapper function reads RNA-seq related datasets from TCGA and GTEx.

Usage

initialize_RNAseq_data()

Details

Its side effects is the global variable TCGA_GTEX_RNAseq_sampletype, which was merged from two internal data frames:

(1) .TCGA_GTEX_RNAseq: the recomputed RNAseq data from both TCGA and GTEx generated by .get_TCGA_GTEX_RNAseq(), which imports the dataset TcgaTargetGtex_RSEM_Hugo_norm_count.

(2) .TCGA_GTEX_sampletype annotates the feature for each sample from TCGA and GTEx. The data frame imports the TcgaTargetGTEX_phenotype.txt dataset and performed basic data cleaning steps including removal of duplicates and NAs.

To reduce the data size, we only select the following four relevant columns out of TcgaTargetGTEX_phenotype.txt to construct .TCGA_GTEX_sampletype.

• sample.type column that annotates malignant of normal tissues

• primary.disease column that annotates cancer types for each sample

• primary.site column that annotates the tissue types

• study column that annotates the cohort “TCGA” or “GTEx”

TCGA_GTEX_RNAseq_sampletype was stored as TCGA_GTEX_RNAseq_sampletype.csv in ~/Documents/EIF_output/ProcessedData folder.

See Also

Other wrapper function for data initialization: initialize_cnv_data(), initialize_data(), initialize_phosphoproteomics_data(), initialize_proteomics_data(), initialize_survival_data()

Examples

## Not run: 
initialize_RNAseq_data()

## End(Not run)

a3609640/eIF4F.analysis documentation built on Jan. 2, 2023, 11:19 p.m.