Trying to plot Kaplan–Meier estimator for a given Ensembl Gene ID (ENSG) using Subjects with expression+clinical data in MMRF-COMMPASS

install dependencies

install.packages("devtools")
devtools::install_github(c("RDocTaskForce/testextra","RDocTaskForce/parsetools","halpo/purrrogress"))
install.packages(c("BiocManager","shiny","markdown","knitr","sweave","xtable","DT","httpuv","sourcetools"))
BiocManager::install(c("EDASeq","genefilter","sva","limma","GenomicFeatures","GenomeInfoDb","GenomicRanges","SummarizedExperiment","EnsDb.Hsapiens.v79","S4Vectors","biomaRt","BiocStyle","edgeR","IRanges","TCGAbiolinks"))

finally install MMRFBiolinks

devtools::install_github("marziasettino/MMRFBiolinks")

download and process expression+clinical data in MMRF-COMMPASS

library(shiny)
library(SummarizedExperiment)
library(dplyr)
library(DT)
library(ggplot2)
library(TCGAbiolinks)
library(MMRFBiolinks)
MMRFclin <- MMRFGDC_QueryClinic(type = "clinical")
listSamples <- MMRFclin$bcr_patient_barcode
query <- GDCquery(project = "MMRF-COMMPASS",data.category = "Transcriptome Profiling",data.type = "Gene Expression Quantification",experimental.strategy = "RNA-Seq",workflow.type="HTSeq - FPKM",barcode = listSamples)
GDCdownload(query, method = "api", files.per.chunk = 10)
MMRnaseqSE <- MMRFGDC_prepare(query,save = TRUE ,save.filename = "GDCdata.rda",directory = "GDCdata",summarizedExperiment = TRUE)
MMRFdataPrepro <- TCGAanalyze_Preprocessing(MMRnaseqSE)
save(file="MMRFdataPrepro.rds",MMRFdataPrepro)
save(file="MMRFclin.rds",MMRFclin)
savehistory("R.history")

run shiny/app and provide ENSG ID in GUI for gene/protein of interest, e.g. ENSG00000196976

runApp('plotKM')

MMRFBiolinks

An R package that extends TCGABiolink package for integrative analysis with MMRF-COMMPASS data

MMRFBiolinks extends TCGABiolink package for searching, downloading and analyzing MMRF-COMMPASS data available at the NCI’s Genomic Data Commons (GDC) Data Portal.

Installation

Once R (version “4.0”) has been started, you can install the released version of MMRFBiolinks from GitHub with:

devtools::install_github("marziasettino/MMRFBiolinks", build_vignettes = TRUE)
library(MMRFBiolinks)

Required libraries

library(TCGAbiolinks)
library(SummarizedExperiment)
library(dplyr)
library(DT)
library(ggplot2)

Vignettes

A list of all currently integrated vignettes can be obtained through:

vignette(package="MMRFBiolinks")

The best way to view vignettes is in your web browser:

devtools::load_all(".")
browseVignettes("MMRFBiolinks")

Get the list of the example data sets

data(package = "MMRFBiolinks")