eIF4F_analysis

Library installation

Load eIF4F.analysis library.

# install eIF4F.analysis package 
devtools::install_github("a3609640/eIF4F.analysis")
# load eif4F.analysis   
library(eIF4F.analysis)

Library initialization

Create output directories

Run the initialize_dir() command to create the sub-directories under ~/Documents/EIF_output to store the output files.

initialize_dir()

Define font format

Load the font types, size and orientation for plotting functions.

initialize_format()

Load omics datasets

Load all needed TCGA, GTEX, CPTAC and CCLE datasets download by Download.sh for the following analyses.

initialize_data()

12 global variables will be saved at csv files under ~/eIF4F.analysis/eIF4F_output/ProcessedData

Perform CNV analysis

EIF4F_CNV_analysis()

Results will be saved as following

Perform differential gene expression/ratio analysis

EIF4F_DEG_analysis()

Perform gene expression and survival analysis

EIF4F_Survival_analysis()

Perform PCA

EIF4F_PCA()

Perform correlating gene analysis

EIF4F_Corrgene_analysis()

Perform RNA protein expression correlation analysis

EIF4F_RNA_pro_correlation()

Perform (phospho)proteomics analysis

EIF4F_Proteomics_analysis()