TrainingSet_Sample_sheet: Sample sheet for the 442 TCGA samples used as training set.

In ijcBIT/cnv.methyl: cnv.methyl finds copy number alteration from methylation idat files

Sample sheet for the 442 TCGA samples used as training set.

Description

A dataset containing the IDs & paths to the 450k microarrays used as training set to infer the reference KCN as described in the paper. Reference ASCAT data needed to estimate each KCN is extracted from a previous work https://github.com/riazn/biallelic_hr.git.

A dataset containing the IDs & paths to the 450k microarrays used as training set to infer the reference KCN as described in the paper. Reference ASCAT data needed to estimate each KCN is extracted from a previous work https://github.com/riazn/biallelic_hr.git.

Usage

data(TrainingSet_Sample_sheet)

data(all_CN_ASCAT)

Format

A data frame with 442 rows and 10 variables:

Sample_Name

Unique identifier of the sample. TCGA barcode, 28 chars

filenames

location of the idat files for each sample

Cancer

Primary Cancer Site

Purity_Impute_RFPurify(Absolute)

Imputed purity from the array

Purity_ASCAT

Purity ref. value Purity predicted from SNPs array.

ASCAT_Amp

Amplified genes (5 to 10 copies) called by ASCAT

ASCAT_Amp10

Largely amplified genes (> 10 copies) called by ASCAT

ASCAT_Gain

Gains (3 & 4 copies) called by ASCAT

ASCAT_HetLoss

Missing 1 allele (1 copy) called by ASCAT

ASCAT_HomDel

Deleted gene in both alleles (0 copies)by ASCAT

A data frame with 442 rows and 10 variables:

Project

Cancer project name ex: TCGA-cancer

barcodes

Unique identifier of the sample. TCGA barcode, 12 chars

ASCAT.path

Path to origin file with CN calls

gene_name

Copy number state called by ASCAT for gene_name

Source

https://github.com/riazn/biallelic_hr.git

https://github.com/riazn/biallelic_hr.git

ijcBIT/cnv.methyl documentation built on Jan. 10, 2023, 7:51 a.m.