NGStestdata: Mutation Annotation Data with Test Set Samples

In MSIseq: Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations

Description

This is a data frame based on the TCGA "mutation annotation file" format.

Usage

data(NGStestdata)

Format

A data frame with 72,111 observations on the following 5 variables:

Chrom

a character vector that indicates the chromosome identifier without the "chr" prefix: "1", "2", ..., "22", "X", "Y"

Start_Position

a numeric vector

End_Position

a numeric vector

Variant_Type

a character vector that indicates the type of variant; legal values are "SNP", "INS" and "DEL". Other values will cause the Compute.input.variables to generate an error

Tumor_Sample_Barcode

the sample ID as a character vector

Any other columns are ignored.

Details

This is sample input data for the Compute.input.variables function.

Source

https://tcga-data.nci.nih.gov/tcga/

References

Mutation Annotation File Format https://wiki.nci.nih.gov/display/TCGA/File+Format+Specifications

MSIseq documentation built on May 2, 2019, 7:23 a.m.