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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

eIF4F.analysis

eIF4F.analysis is an R-based computational pipeline to understand function and regulation of interactions among translation initiation complex proteins across tumor types. This package provides a toolkit for analyses including copy number status, prognosis, subunit abundance and stoichiometry, gene coexpression and pathway activity, and mRNA/protein correlation, all using publicly available multi-omics data.

Before you begin

Perform the following steps to ensure the proper operation of this package.

[System requirements]

[Install R/RStudio]

[Install dependent libraries]

[Install eIF4F analysis package]

[Clone the repository files]

[Download datasets]

[Perform Analyses]

[Tutorial]

[Session information]

[Reference]

System requirements

This project makes use of various resource-intensive R packages, which carries relatively high demands for compute, RAM, and disk I/O resources (but not for graphics resources). Nonetheless, the necessary hardware is attainable in high-end consumer-grade systems.

Description of development systems

The following systems have been used to execute the R scripts in this project:

(verified) System76 "Serval" mobile workstation
- Intel i7-8700k CPU
- 64GB RAM (DDR4-3000, non-ECC)
- Samsung NVMe Pro SSD
- Pop!_OS 22.04 LTS
- RStudio
- R 4.2.1
(verified) PowerSpec G460 desktop computer
- Intel i7-8700k CPU
- 64GB RAM (DDR4-3200, non-ECC)
- Intel M.2 SATA SSD
- Samsung NVMe Evo+ SSD
- Windows 10 Pro
- RStudio for Windows
- R 4.0.3
PowerSpec B748 desktop computer (with aftermarket upgrades)
- Intel i7-12700k CPU
- 128GB RAM (DDR4-3600, non-ECC)
- Sabrent SB-RKT4P-8TB NVMe (gen4) SSD (Pop!_OS installation)
- Seagate FireCuda 530 ZP4000GM30023 NVMe (gen4) SSD (Windows installation)
- NVIDIA GeForce RTX 3090
- Pop!_OS 22.04 LTS
- Windows 11 Pro build 22000.1042
- RStudio 2022.07.2+576 "Spotted Wakerobin" Release
  - (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for Windows
  - Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko)
  - QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
- R-4.2.1 for Windows (Windows native)
- Git for Windows version 2.37.3.windows.1
- Windows Subsystem for Linux
  - Ubuntu 22.04
  - R-4.1.2

System 1 is the reference system on which most development and testing were performed. Additional details of System 1 are provided in the "Session Information" section below. We recommend Linux OS to run the package.

See also README_WINDOWS.md for details regarding observed behavior on Windows.

Additional details of these environments are provided in the "Session Information" section below.

Install R/RStudio

Download & install R 4.2.1, if not already installed.
Download & install RStudio, if not already installed. https://www.rstudio.com/products/rstudio/download/

Install dependent libraries

The required packages will be automatically installed at the first time you run eIF4F.analysis. The following commands are useful to install dependent R packages manually.

# use Bioconductor version 3.15 for package installation
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.15")

# install required packages
bio_pkgs <- c("AnnotationDbi", "circlize",  "clusterProfiler",
              "ComplexHeatmap", "corrplot", "data.table", "devtools",
              "dplyr", "EnvStats", "eulerr", "factoextra",
              "FactoMineR", "forcats", "forestplot", "ggfortify",
              "ggplot2", "ggpubr", "graphics", "grDevices", "grid",
              "limma", "log4r","missMDA", "org.Hs.eg.db", "purrr",
              "RColorBrewer", "ReactomePA", "RCurl","readr", "readxl",
              "reshape2", "R.utils", "scales", "stats", "stringr",
              "survival", "survivalAnalysis", "tibble", "tidyr",
              "tidyselect", "utils")
BiocManager::install(bio_pkgs)

# load required packages
lapply(bio_pkgs, require, character.only = TRUE)

Install eIF4F analysis package

Please install the development version of eIF4F.analysis from GitHub and load it in the R console.

# Install eIF4F.analysis package 
devtools::install_github("a3609640/eIF4F.analysis")

# Load eIF4F.analysis package 
library(eIF4F.analysis)

Clone the repository files

Open the terminal and run the following command line to clone our GitHub repository for eIF4F.analysis under the home directory.

```{bash, eval = FALSE} $ git clone https://github.com/a3609640/eIF4F.analysis

The package files will be stored under `~/eIF4F.analysis`. The cloned repository contains the following files and folders.

![](man/figures/eIF4F.analysis.png){width="240"}

Under the `~/eIF4F.analysis/Script` folder, two R scripts `Download.R` and `Analysis.R` are stored for acquiring datasets and performing analysis.

![](man/figures/eIF4F.analysis.script.png){width="224"}

Open `Download.R` file in RStudio, verify the directories for input and output files as following. These two directory paths are also set inside the package (in `Load.R`), and the values must agree in both places. The descriptions of the steps that follow assume the use of the default `eIF4F_output` location. 

``` r
# default directory for data download and output storage
data_file_directory <- Sys.getenv(c("DATA_FILE_DIRECTORY"), unset = "~/eIF4F.analysis/eIF4F_data")
output_directory <- Sys.getenv(c("OUTPUT_DIRECTORY"), unset = "~/eIF4F.analysis/eIF4F_output")

Download datasets

Download.R downloads all needed datasets (TGCA, GTEx, CPTAC, CCLE, etc.) from URLs and decompresses them. To run the Download.R file in RStudio with the following command line.

source("~/eIF4F.analysis/Script/Download.R")

Download.R will (unless modified) create ~/eIF4F.analysis/eIF4F_data, where all needed datasets (TGCA, GTEx, CPTAC, CCLE etc.) will be stored and decompressed, and ~/eIF4F.analysis/eIF4F_output, where all the analyzed results will be stored.

{width="240"}

After the completion of the download and unzip steps, the eIF4F_data folder contains 16 data files, with a collective size of 15GB.

{width="627"}

Perform Analyses

Analysis.R contains ten exported functions in the package to initialize package and execute all analyses presented in (Wu and Wagner, 2021). The users can simply execute the following command in RStudio to get all analyses performed.

source("~/eIF4F.analysis/Script/Analysis.R")

Analysis results to be automatically stored under ~/eIF4F.analysis/eIF4F_data/ in eight sub-directories.

{width="266"}

Tutorial

Tutorial of executing each function from Analysis.R is available at https://a3609640.github.io/eIF4F.analysis/articles/eIF4F_analysis.html

Documentations for exported and internal function are available at https://a3609640.github.io/eIF4F.analysis/reference/index.html

Session information

The version information of R, Linux and attached or loaded packages for developing this package is the following.

> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.1 (2022-06-23)
 os       Pop!_OS 22.04 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language en_US:en
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2022-10-05
 rstudio  2022.07.1+554 Spotted Wakerobin (desktop)
 pandoc   2.9.2.1 @ /usr/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────
 package          * version  date (UTC) lib source
 abind              1.4-5    2016-07-21 [1] CRAN (R 4.2.0)
 AnnotationDbi    * 1.58.0   2022-04-26 [1] Bioconductor
 ape                5.6-2    2022-03-02 [1] CRAN (R 4.2.0)
 aplot              0.1.7    2022-09-06 [1] CRAN (R 4.2.1)
 assertthat         0.2.1    2019-03-21 [1] CRAN (R 4.2.0)
 backports          1.4.1    2021-12-13 [1] CRAN (R 4.2.0)
 Biobase          * 2.56.0   2022-04-26 [1] Bioconductor
 BiocGenerics     * 0.42.0   2022-04-26 [1] Bioconductor
 BiocParallel       1.30.3   2022-06-05 [1] Bioconductor
 Biostrings         2.64.1   2022-08-18 [1] Bioconductor
 bit                4.0.4    2020-08-04 [1] CRAN (R 4.2.0)
 bit64              4.0.5    2020-08-30 [1] CRAN (R 4.2.0)
 bitops             1.0-7    2021-04-24 [1] CRAN (R 4.2.0)
 blob               1.2.3    2022-04-10 [1] CRAN (R 4.2.0)
 broom              1.0.1    2022-08-29 [1] CRAN (R 4.2.1)
 cachem             1.0.6    2021-08-19 [1] CRAN (R 4.2.0)
 car                3.1-0    2022-06-15 [1] CRAN (R 4.2.0)
 carData            3.0-5    2022-01-06 [1] CRAN (R 4.2.0)
 cellranger         1.1.0    2016-07-27 [1] CRAN (R 4.2.0)
 checkmate          2.1.0    2022-04-21 [1] CRAN (R 4.2.0)
 circlize           0.4.15   2022-05-10 [1] CRAN (R 4.2.0)
 cli                3.4.1    2022-09-23 [1] CRAN (R 4.2.1)
 clue               0.3-61   2022-05-30 [1] CRAN (R 4.2.0)
 cluster            2.1.4    2022-08-22 [1] CRAN (R 4.2.1)
 clusterProfiler    4.4.4    2022-06-21 [1] Bioconductor
 codetools          0.2-18   2020-11-04 [4] CRAN (R 4.2.0)
 colorspace         2.0-3    2022-02-21 [1] CRAN (R 4.2.0)
 ComplexHeatmap     2.12.1   2022-08-09 [1] Bioconductor
 corrplot           0.92     2021-11-18 [1] CRAN (R 4.2.0)
 cowplot            1.1.1    2020-12-30 [1] CRAN (R 4.2.0)
 crayon             1.5.2    2022-09-29 [1] CRAN (R 4.2.1)
 data.table         1.14.2   2021-09-27 [1] CRAN (R 4.2.0)
 DBI                1.1.3    2022-06-18 [1] CRAN (R 4.2.0)
 digest             0.6.29   2021-12-01 [1] CRAN (R 4.2.0)
 DO.db              2.9      2022-06-07 [1] Bioconductor
 doParallel         1.0.17   2022-02-07 [1] CRAN (R 4.2.0)
 DOSE               3.22.1   2022-08-30 [1] Bioconductor
 downloader         0.4      2015-07-09 [1] CRAN (R 4.2.0)
 dplyr              1.0.10   2022-09-01 [1] CRAN (R 4.2.1)
 DT                 0.25     2022-09-12 [1] CRAN (R 4.2.1)
 eIF4F.analysis   * 0.1.0    2022-10-10 [1] local
 ellipsis           0.3.2    2021-04-29 [1] CRAN (R 4.2.0)
 emmeans            1.8.1-1  2022-09-08 [1] CRAN (R 4.2.1)
 enrichplot         1.16.2   2022-08-30 [1] Bioconductor
 EnvStats           2.7.0    2022-03-07 [1] CRAN (R 4.2.0)
 estimability       1.4.1    2022-08-05 [1] CRAN (R 4.2.1)
 eulerr             6.1.1    2021-09-06 [1] CRAN (R 4.2.0)
 factoextra         1.0.7    2020-04-01 [1] CRAN (R 4.2.0)
 FactoMineR         2.6      2022-09-09 [1] CRAN (R 4.2.1)
 fansi              1.0.3    2022-03-24 [1] CRAN (R 4.2.0)
 farver             2.1.1    2022-07-06 [1] CRAN (R 4.2.0)
 fastmap            1.1.0    2021-01-25 [1] CRAN (R 4.2.0)
 fastmatch          1.1-3    2021-07-23 [1] CRAN (R 4.2.0)
 fgsea              1.22.0   2022-04-26 [1] Bioconductor
 flashClust         1.01-2   2012-08-21 [1] CRAN (R 4.2.0)
 forcats            0.5.2    2022-08-19 [1] CRAN (R 4.2.1)
 foreach            1.5.2    2022-02-02 [1] CRAN (R 4.2.0)
 forestplot         3.1.0    2022-10-09 [1] CRAN (R 4.2.1)
 generics           0.1.3    2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb       1.32.4   2022-09-06 [1] Bioconductor
 GenomeInfoDbData   1.2.8    2022-06-07 [1] Bioconductor
 GetoptLong         1.0.5    2020-12-15 [1] CRAN (R 4.2.0)
 ggforce            0.4.1    2022-10-04 [1] CRAN (R 4.2.1)
 ggfortify          0.4.14   2022-01-03 [1] CRAN (R 4.2.0)
 ggfun              0.0.7    2022-08-31 [1] CRAN (R 4.2.1)
 ggplot2            3.3.6    2022-05-03 [1] CRAN (R 4.2.0)
 ggplotify          0.1.0    2021-09-02 [1] CRAN (R 4.2.0)
 ggpubr             0.4.0    2020-06-27 [1] CRAN (R 4.2.0)
 ggraph             2.0.6    2022-08-08 [1] CRAN (R 4.2.1)
 ggrepel            0.9.1    2021-01-15 [1] CRAN (R 4.2.0)
 ggsignif           0.6.3    2021-09-09 [1] CRAN (R 4.2.0)
 ggtree             3.4.2    2022-08-14 [1] Bioconductor
 GlobalOptions      0.1.2    2020-06-10 [1] CRAN (R 4.2.0)
 glue               1.6.2    2022-02-24 [1] CRAN (R 4.2.0)
 GO.db              3.15.0   2022-06-07 [1] Bioconductor
 GOSemSim           2.22.0   2022-04-26 [1] Bioconductor
 graph              1.74.0   2022-04-26 [1] Bioconductor
 graphite           1.42.0   2022-04-26 [1] Bioconductor
 graphlayouts       0.8.2    2022-09-29 [1] CRAN (R 4.2.1)
 gridExtra          2.3      2017-09-09 [1] CRAN (R 4.2.0)
 gridGraphics       0.5-1    2020-12-13 [1] CRAN (R 4.2.0)
 gtable             0.3.1    2022-09-01 [1] CRAN (R 4.2.1)
 hms                1.1.2    2022-08-19 [1] CRAN (R 4.2.1)
 htmltools          0.5.3    2022-07-18 [1] CRAN (R 4.2.1)
 htmlwidgets        1.5.4    2021-09-08 [1] CRAN (R 4.2.0)
 httr               1.4.4    2022-08-17 [1] CRAN (R 4.2.1)
 igraph             1.3.5    2022-09-22 [1] CRAN (R 4.2.1)
 IRanges          * 2.30.1   2022-08-18 [1] Bioconductor
 iterators          1.0.14   2022-02-05 [1] CRAN (R 4.2.0)
 jsonlite           1.8.2    2022-10-02 [1] CRAN (R 4.2.1)
 KEGGREST           1.36.3   2022-07-12 [1] Bioconductor
 km.ci              0.5-6    2022-04-06 [1] CRAN (R 4.2.0)
 KMsurv             0.1-5    2012-12-03 [1] CRAN (R 4.2.0)
 knitr              1.40     2022-08-24 [1] CRAN (R 4.2.1)
 labeling           0.4.2    2020-10-20 [1] CRAN (R 4.2.0)
 lattice            0.20-45  2021-09-22 [4] CRAN (R 4.2.0)
 lazyeval           0.2.2    2019-03-15 [1] CRAN (R 4.2.0)
 leaps              3.1      2020-01-16 [1] CRAN (R 4.2.0)
 lifecycle          1.0.3    2022-10-07 [1] CRAN (R 4.2.1)
 limma              3.52.3   2022-09-11 [1] Bioconductor
 log4r              0.4.2    2021-11-04 [1] CRAN (R 4.2.1)
 magrittr           2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
 MASS               7.3-58.1 2022-08-03 [1] CRAN (R 4.2.1)
 Matrix             1.5-1    2022-09-13 [1] CRAN (R 4.2.1)
 matrixStats        0.62.0   2022-04-19 [1] CRAN (R 4.2.0)
 memoise            2.0.1    2021-11-26 [1] CRAN (R 4.2.0)
 mgcv               1.8-40   2022-03-29 [4] CRAN (R 4.2.0)
 mice               3.14.0   2021-11-24 [1] CRAN (R 4.2.0)
 missMDA            1.18     2020-12-11 [1] CRAN (R 4.2.0)
 multcomp           1.4-20   2022-08-07 [1] CRAN (R 4.2.1)
 multcompView       0.1-8    2019-12-19 [1] CRAN (R 4.2.1)
 munsell            0.5.0    2018-06-12 [1] CRAN (R 4.2.0)
 mvtnorm            1.1-3    2021-10-08 [1] CRAN (R 4.2.0)
 nlme               3.1-159  2022-08-09 [1] CRAN (R 4.2.1)
 org.Hs.eg.db     * 3.15.0   2022-06-07 [1] Bioconductor
 patchwork          1.1.2    2022-08-19 [1] CRAN (R 4.2.1)
 pillar             1.8.1    2022-08-19 [1] CRAN (R 4.2.1)
 pkgconfig          2.0.3    2019-09-22 [1] CRAN (R 4.2.0)
 plyr               1.8.7    2022-03-24 [1] CRAN (R 4.2.0)
 png                0.1-7    2013-12-03 [1] CRAN (R 4.2.0)
 polyclip           1.10-0   2019-03-14 [1] CRAN (R 4.2.0)
 polylabelr         0.2.0    2020-04-19 [1] CRAN (R 4.2.0)
 purrr              0.3.5    2022-10-06 [1] CRAN (R 4.2.1)
 qvalue             2.28.0   2022-04-26 [1] Bioconductor
 R.methodsS3        1.8.2    2022-06-13 [1] CRAN (R 4.2.0)
 R.oo               1.25.0   2022-06-12 [1] CRAN (R 4.2.0)
 R.utils            2.12.0   2022-06-28 [1] CRAN (R 4.2.1)
 R6                 2.5.1    2021-08-19 [1] CRAN (R 4.2.0)
 ragg               1.2.3    2022-09-29 [1] CRAN (R 4.2.1)
 rappdirs           0.3.3    2021-01-31 [1] CRAN (R 4.2.0)
 RColorBrewer       1.1-3    2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp               1.0.9    2022-07-08 [1] CRAN (R 4.2.0)
 RCurl              1.98-1.9 2022-10-03 [1] CRAN (R 4.2.1)
 reactome.db        1.81.0   2022-07-15 [1] Bioconductor
 ReactomePA         1.40.0   2022-04-26 [1] Bioconductor
 readr              2.1.3    2022-10-01 [1] CRAN (R 4.2.1)
 readxl             1.4.1    2022-08-17 [1] CRAN (R 4.2.1)
 reshape2           1.4.4    2020-04-09 [1] CRAN (R 4.2.0)
 rjson              0.2.21   2022-01-09 [1] CRAN (R 4.2.0)
 rlang              1.0.6    2022-09-24 [1] CRAN (R 4.2.1)
 RSQLite            2.2.18   2022-10-04 [1] CRAN (R 4.2.1)
 rstatix            0.7.0    2021-02-13 [1] CRAN (R 4.2.0)
 rstudioapi         0.14     2022-08-22 [1] CRAN (R 4.2.1)
 S4Vectors        * 0.34.0   2022-04-26 [1] Bioconductor
 sandwich           3.0-2    2022-06-15 [1] CRAN (R 4.2.1)
 scales             1.2.1    2022-08-20 [1] CRAN (R 4.2.1)
 scatterpie         0.1.8    2022-09-03 [1] CRAN (R 4.2.1)
 scatterplot3d      0.3-42   2022-09-08 [1] CRAN (R 4.2.1)
 sessioninfo        1.2.2    2021-12-06 [1] CRAN (R 4.2.0)
 shadowtext         0.1.2    2022-04-22 [1] CRAN (R 4.2.0)
 shape              1.4.6    2021-05-19 [1] CRAN (R 4.2.0)
 stringi            1.7.8    2022-07-11 [1] CRAN (R 4.2.0)
 stringr            1.4.1    2022-08-20 [1] CRAN (R 4.2.1)
 survival           3.4-0    2022-08-09 [4] CRAN (R 4.2.1)
 survivalAnalysis   0.3.0    2022-02-11 [1] CRAN (R 4.2.0)
 survminer          0.4.9    2021-03-09 [1] CRAN (R 4.2.0)
 survMisc           0.5.6    2022-04-07 [1] CRAN (R 4.2.0)
 systemfonts        1.0.4    2022-02-11 [1] CRAN (R 4.2.0)
 textshaping        0.3.6    2021-10-13 [1] CRAN (R 4.2.0)
 TH.data            1.1-1    2022-04-26 [1] CRAN (R 4.2.1)
 tibble             3.1.8    2022-07-22 [1] CRAN (R 4.2.1)
 tidygraph          1.2.2    2022-08-22 [1] CRAN (R 4.2.1)
 tidyr              1.2.1    2022-09-08 [1] CRAN (R 4.2.1)
 tidyselect         1.1.2    2022-02-21 [1] CRAN (R 4.2.0)
 tidytidbits        0.3.2    2022-03-16 [1] CRAN (R 4.2.0)
 tidytree           0.4.1    2022-09-26 [1] CRAN (R 4.2.1)
 treeio             1.20.2   2022-08-14 [1] Bioconductor
 tweenr             2.0.2    2022-09-06 [1] CRAN (R 4.2.1)
 tzdb               0.3.0    2022-03-28 [1] CRAN (R 4.2.0)
 utf8               1.2.2    2021-07-24 [1] CRAN (R 4.2.0)
 vctrs              0.4.2    2022-09-29 [1] CRAN (R 4.2.1)
 viridis            0.6.2    2021-10-13 [1] CRAN (R 4.2.0)
 viridisLite        0.4.1    2022-08-22 [1] CRAN (R 4.2.1)
 vroom              1.6.0    2022-09-30 [1] CRAN (R 4.2.1)
 withr              2.5.0    2022-03-03 [1] CRAN (R 4.2.0)
 xfun               0.33     2022-09-12 [1] CRAN (R 4.2.1)
 xtable             1.8-4    2019-04-21 [1] CRAN (R 4.2.0)
 XVector            0.36.0   2022-04-26 [1] Bioconductor
 yulab.utils        0.0.5    2022-06-30 [1] CRAN (R 4.2.0)
 zlibbioc           1.42.0   2022-04-26 [1] Bioconductor
 zoo                1.8-11   2022-09-17 [1] CRAN (R 4.2.1)

 [1] /home/suwu/R/x86_64-pc-linux-gnu-library/4.2
 [2] /usr/local/lib/R/site-library
 [3] /usr/lib/R/site-library
 [4] /usr/lib/R/library

──────────────────────────────────────────────────────────────────────

Reference

Wu, Su, and Gerhard Wagner. 2021. "Deep Computational AnalysisDetails Dysregulation of Eukaryotic Translation Initiation Complex eIF4Fin Human Cancers." Cell Systems 12 (9): 907--923.e6. https://doi.org/10.1016/j.cels.2021.07.002.
Wu, Su, and Gerhard Wagner. 2022. "Protocol to AnalyzeDysregulation of the eIF4F Complex in Human Cancers Using R Software andLarge Public Datasets." STAR Protocols 3 (4): 101880. https://doi.org/10.1016/j.xpro.2022.101880.

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

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

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

eIF4F.analysis

Before you begin

System requirements

Description of development systems

Install R/RStudio

Install dependent libraries

Install eIF4F analysis package

Clone the repository files

Download datasets

Perform Analyses

Tutorial

Session information

Reference

R Package Documentation

Browse R Packages

We want your feedback!

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

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

eIF4F.analysis

Before you begin

System requirements

Description of development systems

Install R/RStudio

Install dependent libraries

Install eIF4F analysis package

Clone the repository files

Download datasets

Perform Analyses

Tutorial

Session information

Reference

R Package Documentation

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