A wrapper function to read RNA-seq and survival datasets from TCGA.
initialize_survival_data()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.
Other wrapper function for data initialization:
initialize_RNAseq_data(),
initialize_cnv_data(),
initialize_data(),
initialize_phosphoproteomics_data(),
initialize_proteomics_data()
if (FALSE) {
initialize_survival_data()
}