README.md

In Solatar/cgAnalyzR:

Installation

devtools::install_github("solatar/cganalyzr")

Get Data

This part completely relies on the cgdsr package. Check out their documentation and function overview.

First build the cgds object. The output is the same that you would get with cgdsr::CGDS("https://www.cbioportal.org/"). The cgBase function additionally prints out all the possible studies to choose from. Define one of them as your study.

library(cgAnalyzR)
cgds <- cgBase()
mystudy <- "laml_tcga"

Now check what data types are available for your study, via the cgStudy function. This prints out 2 tables, one with the profiles (type of experiments) and the caselists (what samples are available for what experiment type). Then get the data of your choice via the cgData function, providing the profile_name of your choice from the previous printout. You can also specify the caselist to be used. The default for this function takes all samples, but you can specify this in the caselist_name arguement.

cgStudy(cgds, mystudy)
mydata <- cgData(cgds, mystudy, profile_name = "mRNA expression (RNA Seq RPKM)")

To get mutation data, the cgMutation does this in the same way as the cgData function, just with fixed profile_name and caselist_name.

mymutation <- cgMutation(cgds, mystudy, genes = c("FLT3","TP53"))

Solatar/cgAnalyzR documentation built on Feb. 15, 2021, 12:18 a.m.