NGStestdata


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


datasets

A decision tree classifier for detecting microsatellite instability (MSI) in somatic mutation data from whole exome sequencing. MSI is detected based on different mutation rates in all sites as well as in simple sequence repeats. This mechanism can also be applied to sequence data of targeted gene panels with shorter sequence length.

Mini Huang

MSIseq

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

NGStestdata function

A data frame with 72,111 observations on the following 5 variables: 
  <dl>
    <dt><code>Chrom</code></dt><dd>a character vector that indicates the chromosome identifier
      without the "chr" prefix: "1", "2", ..., "22", "X", "Y"</dd> <dt><code>Start_Position</code></dt><dd>a numeric vector</dd> <dt><code>End_Position</code></dt><dd>a numeric vector</dd> <dt><code>Variant_Type</code></dt><dd>a character vector that indicates the
      type of variant; legal values are "SNP", "INS" and "DEL". Other
      values will cause the <code><a rd-options="MSIseq:Compute.input.variables" href="/link/Compute.input.variables?package=MSIseq&version=1.0.0&to=MSIseq%3ACompute.input.variables" data-mini-rdoc="MSIseq:Compute.input.variables::Compute.input.variables">Compute.input.variables</a></code> to generate an error</dd> <dt><code>Tumor_Sample_Barcode</code></dt><dd>the sample ID as a character vector</dd> </dl> Any other columns are ignored.

Format

<a href="https://tcga-data.nci.nih.gov/tcga/">https://tcga-data.nci.nih.gov/tcga/</a>

NGStestdata: Mutation Annotation Data with Test Set Samples

Description

Usage

Arguments

Format

Source

Details

References