tcga.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tcga-data.R
\docType{data}
\name{tcga}
\alias{tcga}
\title{TCGA somatic mutation annotation data
from 10 common cancer sites}
\format{
A dataset with 1,395,665 rows and 14 columns:

\describe{
\item{patient_id}{the patient (tumor) label. Obtained by extracting
the first 16 characters of the column'Tumor_Sample_Barcode' in
the original TCGA data.}
\item{Hugo_Symbol}{the gene label}
\item{Chromosome}{Chromosome label}
\item{Variant}{the variant label. Obtained by concatenating
the columns labeled
'Hugo_Symbol', "HGVSp_Short', 'Chromosome', 'Start_Position', 'Tumor_Seq_Allele1',
and 'Tumor_Seq_Allele2' in the original TCGA data}
\item{Start_Position}{Start Position of alteration on the chromosome}
\item{End_Position}{End Position of alteration on the chromosome}
\item{Tumor_Seq_Allele1}{.}
\item{Tumor_Seq_Allele2}{.}
\item{Reference_Allele}{.}
\item{HGVSp_Short}{Protein code of alteration}
\item{Variant_Type}{Type of alteration}
\item{Variant_Classification}{.}
\item{CANCER_HISTOLOGY}{Histological subtype for each tumor}
\item{CANCER_SITE}{Cancer site of origin of each tumor}
}
}
\source{
https://github.com/cBioPortal/datahub
}
\usage{
tcga
}
\description{
A subset of the publicly available NIH's the Cancer Genome Atlas (TCGA)
whole exome sequencing data containing non-synonymous SNV mutations.
More specifically,
the subset of the TCGA data with
\code{Variant_Type == "SNP"} and  tumors from the following 10 cancer sites:
BREAST, COLORECTAL, ESOPHAGEAL, KIDNEY, LIVER,
LUNG, OVARIAN, PANCREATIC, PROSTATE, and SKIN
}
\keyword{datasets}