initialize_survival_data: Read RNA-seq and survival datasets from TCGA

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

Read RNA-seq and survival datasets from TCGA

Description

A wrapper function to read RNA-seq and survival datasets from TCGA.

Usage

initialize_survival_data()

Details

Side effects:

(1) TCGA_RNAseq_OS_sampletype a merged dataset from .TCGA_RNAseq, .TCGA_OS and .TCGA_sampletype.

• .TCGA_RNAseq: the RNAseq data from TCGA generated from .get_TCGA_RNAseq(), which imports the dataset EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.

• .TCGA.OS: the clinical data from Survival_SupplementalTable_S1_20171025_xena_sp. We select three columns: OS for overall survival status, OS.time for overall survival time and sample for sample ID of each patient.

• .TCGA_sampletype: the annotation data from the TCGA_phenotype_denseDataOnlyDownload.tsv dataset. We select two columns sample.type that annotates malignant tissues, and primary.disease that annotates cancer types for each sample.

Only malignant tissue (Solid normal tissues are excluded) are selected for survival analysis

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

See Also

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

Examples

## Not run: 
initialize_survival_data()

## End(Not run)

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