initialize_cnv_data: Read all CNV related datasets from TCGA

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

Read all CNV related datasets from TCGA

Description

A wrapper function reads all CNV related datasets from TCGA and its side effects are three global variables.

Usage

initialize_cnv_data()

Details

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.

See Also

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

Examples

## Not run: 
 initialize_cnv_data()
 
## End(Not run)

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