allele_data_filt: All data files merged

In jhrcook/KrasAlleleCna: The Allele-Specific CNA Analysis of KRAS in CRC

Description

Contains ANNOVAR mutation calls with the number of reads from 'mpileup', copy number of the locus, and purity of the tumor sample. The allele-specific copy number was calculated from those values for each KRAS allele.

Usage

allele_data_filt

Format

a tibble (182 x 25)

common_id

ID shared by all data tables

Chr

chromosome

Start

start of variant

End

end of variant

aa_mod

more usable amino acid change

total_num_reads

total number of reads at this site

num_mut_reads

number of mutant reads

Ref

reference allele

Alt

alternate allele

Func.refGene

where the alteration is

Gene.refGene

gene name

ExonicFunc.refGene

type of mutation

file_name

name of the file

file_id

file ID

project_id

ID of the source project (TCGA-COAD or -READ)

case_id

case ID

sample_id

sample ID

sample_type

from where the sample was taken

CNV_start

start of the CNV call

CNV_end

end of the CNV call

copy_number

copy number at the locus

purity

purity of the tumor sample

cn_mut

copy number of the mutant allele

copy_number_adj

copy number of the locus, adjusted for purity

cn_wt

copy number of the WT allele

jhrcook/KrasAlleleCna documentation built on May 28, 2019, 1:22 p.m.