Package 'TCGAgistic'

Title: Easily access TCGA gistic data
Description: Streams TCGA GISTIC2 copynumber data into the R session.
Authors: Sam El-Kamand [aut, cre]
Maintainer: Sam El-Kamand <[email protected]>
License: MIT + file LICENSE
Version: 0.0.0.9000
Built: 2024-10-27 03:18:30 UTC
Source: https://github.com/CCICB/TCGAgistic

Help Index

List Available Datasets

Description

List Available Datasets

Usage

tcga_gistic_available()

Value

a dataframe listing available datasets

Examples

tcga_gistic_available()

Load TCGA GISTIC data

Description

Load TCGA GISTIC objects into R. Streams data from TCGAgisticDB repo.

Usage

tcga_gistic_load(
  cohort,
  source = "Firehose",
  cnLevel = c("all", "deep", "shallow"),
  verbose = TRUE
)

Arguments

cohort

abbreviation of TCGA cohort See tcga_gistic_available() for valid values (string)
source

source of the data (currently we only support 'Firehose' data (string)
cnLevel

level of CN changes to use. Can be 'all', 'deep' or 'shallow'. Default uses all i.e, genes with both 'shallow' or 'deep' CN changes
verbose

verbosity (flag)

Value

A maftools & CRUX-compatible list of summarized data.

Examples

# Load libraries
library(TCGAgistic)
library(maftools)

# Load dataset
gistic <- tcga_gistic_load("ACC", source = "Firehose", cnLevel = "all")

# Visualise results
gisticChromPlot(gistic)