Read all proteomics related datasets from CCLE and CPTAC LUAD

A wrapper function reads all proteomics related datasets from CCLE and CPTAC LUAD.

initialize_proteomics_data()

Details

Side effects:

(1) CCLE_RNAseq: the RNAseq data of CCLE from the download dataset CCLE_expression_full.csv. It is stored as CCLE_RNAseq.csv in ~/Documents/EIF_output/ProcessedData folder.

(2) CCLE_Anno: the annotation data of CCLE from sample_info.csv. It is stored as CCLE_Anno.csv in ~/Documents/EIF_output/ProcessedData folder.

(3) CCLE_Proteomics: the proteomics data of CCLE from protein_quant_current_normalized.csv. It is stored as CCLE_Proteomics.csv in ~/Documents/EIF_output/ProcessedData folder.

(4) CPTAC_LUAD_Proteomics: the proteomics data with annotation of CPTAC LUAD study from the download data file Protein.xlsx. It is stored as CPTAC_LUAD_Proteomics.csv in ~/Documents/EIF_output/ProcessedData folder.

(5) CPTAC_LUAD_RNAseq: the RNAseq data of CPTAC LUAD samples from the download data file RNA.xlsx. It is stored as CPTAC_LUAD_RNAseq.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_survival_data()

Examples

if (FALSE) {
initialize_proteomics_data()
}