initialize_phosphoproteomics_data: Read all phosphoproteomics related datasets from CPTAC LUAD

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

Read all phosphoproteomics related datasets from CPTAC LUAD

Description

A wrapper function reads all phosphoproteomics related datasets from CPTAC LUAD and its side effects are two global variables.

Usage

initialize_phosphoproteomics_data()

Details

Side effects:

(1) CPTAC_LUAD_Phos: the phosphoproteomics data of CPTAC LUAD from the download data Phos.xlsx.

(2) CPTAC_LUAD_Clinic_Sampletype: a merged dataset from two data frames. It provides the annotation data about sample types (tumor or healthy tissues) and tumors stages of each sample

• .CPTAC_LUAD_Clinic, the CPTAC clinical data from the download dataset S046_BI_CPTAC3_LUAD_Discovery_Cohort_Clinical_Data_r1_May2019.xlsx

• .CPTAC_LUAD_sampletype, the CPTAC annotation data from the download dataset S046_BI_CPTAC3_LUAD_Discovery_Cohort_Samples_r1_May2019.xlsx

CPTAC_LUAD_Phos and CPTAC_LUAD_Clinic_Sampletype are stored as CPTAC_LUAD_Phos.csv and CPTAC_LUAD_Clinic_Sampletype.csv in ~/Documents/EIF_output/ProcessedData folder.

See Also

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

Examples

## Not run: 
initialize_phosphoproteomics_data()

## End(Not run)

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