A wrapper function for data initialization loads the download data files.
initialize_data()initialize_data() runs five data initialization functions
to load the relevant data files.
data initialization functions read datasets and generate twelve global variables
available to functions in the package. Although those global variables are not
accessible to the user and will not show at the users' workspace, this package
has saved them as csv files under ~/Documents/EIF_output/ProcessedData in case
that users would like to access the data frames for their own analyses.
Side effects:
(1) TCGA_CNV_valueimports the download dataset
Gistic2_CopyNumber_Gistic2_all_data_by_genes. It is stored
as TCGA_CNV_value.csv
(2) TCGA_CNV_sampletype imports and merges datasets from
Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes and
TCGA_phenotype_denseDataOnlyDownload.tsv. It is stored
as TCGA_CNV_sampletype.csv
(3) TCGA_CNVratio_sampletype imports and merges datasets from
broad.mit.edu_PANCAN_Genome_Wide_SNP_6_whitelisted.gene.xena and
TCGA_phenotype_denseDataOnlyDownload.tsv. It is stored
as TCGA_CNVratio_sampletype.csv
(4) TCGA_GTEX_RNAseq_sampletype imports and merges datasets from
TcgaTargetGtex_RSEM_Hugo_norm_count and TcgaTargetGTEX_phenotype.txt.
It is stored as TCGA_GTEX_RNAseq_sampletype.csv.
(5) TCGA_RNAseq_OS_sampletype imports and merges datasets from
EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena,
Survival_SupplementalTable_S1_20171025_xena_sp and
TCGA_phenotype_denseDataOnlyDownload.tsv.
It is stored as TCGA_GTEX_RNAseq_sampletype.csv.
(6) CCLE_RNAseq imports the download dataset
CCLE_expression_full.csv. It is stored as CCLE_RNAseq.csv.
(7) CCLE_Annoimports the download dataset sample_info.csv. It is stored
as CCLE_Anno.csv.
(8) CCLE_Proteomics imports the download dataset
protein_quant_current_normalized.csv. It is stored as CCLE_Proteomics.csv.
(9) CPTAC_LUAD_Proteomics imports the download dataset Protein.xlsx.
It is stored as CPTAC_LUAD_Proteomics.csv.
(10) CPTAC_LUAD_RNAseqimports the download dataset RNA.xlsx.
It is stored as CPTAC_LUAD_RNAseq.csv.
(11) CPTAC_LUAD_Phosimports the download dataset Phos.xlsx.
It is stored as CPTAC_LUAD_Phos.csv.
(12) CPTAC_LUAD_Clinic_Sampletype imports and merges datasets from
S046_BI_CPTAC3_LUAD_Discovery_Cohort_Clinical_Data_r1_May2019.xlsx and
S046_BI_CPTAC3_LUAD_Discovery_Cohort_Samples_r1_May2019.xlsx.
It is stored as CPTAC_LUAD_Clinic_Sampletype.csv.
Other wrapper function for data initialization:
initialize_RNAseq_data(),
initialize_cnv_data(),
initialize_phosphoproteomics_data(),
initialize_proteomics_data(),
initialize_survival_data()
if (FALSE) {
initialize_data()
}