import.cosmic.cancer.gene.census.data: Import COSMIC Cancer Gene Census Data

In shlienlab/cosmic.cancer.gene.census: COSMIC cancer gene census dataset and functions.

Description

Import the COSMIC Cancer Gene Census curated list of oncogenes that has been downloaded from https://cancer.sanger.ac.uk/census (requires registration). The downloaded file can either be tab or comman separated values.

Usage

import.cosmic.cancer.gene.census.data(file = NULL, sep = "\t")

Arguments

file	full path to the file containing the tab or comma separated file from https://cancer.sanger.ac.uk/census
sep	delimited used in the file (optional, default: \"\t\")

Value

Returns a dataframe with column "gene" containing the curated oncogenes.

Author(s)

Richard J. de Borja

References

https://cancer.sanger.ac.uk/census

Examples

cosmic.file <- system.file('extdata', 'Census_allWed__Jul__13__14_22_47__2016.tsv', package='cosmic.cancer.gene.census')
cosmic <- import.cosmic.cancer.gene.census.data(file=cosmic.file, sep="\t")

shlienlab/cosmic.cancer.gene.census documentation built on May 20, 2019, 5:27 p.m.