setCGclinic: get clinical data from patients with specific data about...

In Solatar/setR:

Description

Imports: cgdsr

Usage

setCGclinic(cgds, study, profile, caselist, genes)

Arguments

cgds	output from the setCGbase() function
study	ouput from the setCGstudy() function
profile	integer, profile name (what kind of data, RNA-Seq, Mutations, ...) obtained from the printout of the setCGstudy() function
caselist	integer, caselist name (which samples) obtained from the printout of the setCGstudy() function
genes	character vector, genes of interest, Symbols, EntrezIds and EnsemblIds work, maybe others too.

Details

profile and caselist should be logically conntected, e.g. the caselist "samples with mutation data" would go along well with the profile "Mutations"

Value

data.frame, clinical data of the patients (depending on what caselist was chosen) with data about the genes of interest (RNA-Seq counts, mutations occurences) depending on what profile was chosen

Examples

cgds <- setCGbase()
study <- setCGstudy(cgds, 5)
clinic <- setCGclinic(cgds, study, 2, 1, c("ACTA1","HOXA9"))

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.