A wrapper function reads all CNV related datasets from TCGA and its side effects are three global variables.
initialize_cnv_data()Side effects:
(1) TCGA_CNV_value: the unthreshold CNV value data generated as the output
.get_TCGA_CNV_value(), which imports the download dataset
Gistic2_CopyNumber_Gistic2_all_data_by_genes.
(2) TCGA_CNV_sampletype: the merged dataset from
.TCGA.CNV that contains the threshold CNV data from the download dataset
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes and was generated
from .get_TCGA_CNV(),
.TCGA_sampletype that contains the annotation data from
TCGA_phenotype_denseDataOnlyDownload.tsv with the selection of
sample.type and primary.disease columns. Solid Tissue Normal samples
are excluded.
(3) TCGA_CNVratio_sampletype: the merged dataset from
.TCGA_CNV_ratio that contains the CNV ratio data from the download
dataset broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena and
was generated by .get_TCGA_CNV_ratio(),
.TCGA_sampletype.
TCGA_CNV_value, TCGA_CNV_sampletype and TCGA_CNVratio_sampletype are
stored as TCGA_CNV_value.csv, TCGA_CNV_sampletype.csv and
TCGA_CNVratio_sampletype.csv in ~/Documents/EIF_output/ProcessedData folder.
Other wrapper function for data initialization:
initialize_RNAseq_data(),
initialize_data(),
initialize_phosphoproteomics_data(),
initialize_proteomics_data(),
initialize_survival_data()
if (FALSE) {
initialize_cnv_data()
}