allele_depth_tib: mpileup and ANNOVAR data merged

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

Description

A tibble of both mpileup and ANNOVAR data - thus it holds the number of reads at each mutations

Usage

allele_depth_tib

Format

a tibble (190 x 23)

file_id

file ID

Chr

chromosome

Start

start of variant

End

end of variant

Ref

reference allele

Alt

alternate allele

Func.refGene

where the alteration is

Gene.refGene

gene name

GeneDetail.refGene

ExonicFunc.refGene

type of mutation

AAChange.refGene

amino acid change

aa_mod

more usable amino acid change

total_num_reads

total number of reads

num_mut_reads

number of mutant allele reads

file_name

name of the file

data_category

category of data (are all "Sequencing Reads")

data_type

type of data (are all "Aligned Reads")

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

keep

which bam file to keep

downloaded

logical for if the file was downloaded successfully

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