tcga: TCGA somatic mutation annotation data from 10 common cancer...

In c7rishi/hidgenclassifier: Functions for Bayesian hierarchical hidden genome classifier

TCGA somatic mutation annotation data from 10 common cancer sites

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 Variant_Type == "SNP" and tumors from the following 10 cancer sites: BREAST, COLORECTAL, ESOPHAGEAL, KIDNEY, LIVER, LUNG, OVARIAN, PANCREATIC, PROSTATE, and SKIN

Usage

tcga

Format

A dataset with 1,395,665 rows and 14 columns:

patient_id

the patient (tumor) label. Obtained by extracting the first 16 characters of the column'Tumor_Sample_Barcode' in the original TCGA data.

Hugo_Symbol

the gene label

Chromosome

Chromosome label

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

Start_Position

Start Position of alteration on the chromosome

End_Position

End Position of alteration on the chromosome

Tumor_Seq_Allele1

.

Tumor_Seq_Allele2

.

Reference_Allele

.

HGVSp_Short

Protein code of alteration

Variant_Type

Type of alteration

Variant_Classification

.

CANCER_HISTOLOGY

Histological subtype for each tumor

CANCER_SITE

Cancer site of origin of each tumor

Source

https://github.com/cBioPortal/datahub

c7rishi/hidgenclassifier documentation built on June 14, 2024, 11:10 a.m.