train.mutationNum


This is a data frame containing the counts of 9 mutation types for each sample in <code><a rd-options="MSIseq:NGStraindata" href="/link/NGStraindata?package=MSIseq&version=1.0.0&to=MSIseq%3ANGStraindata" data-mini-rdoc="MSIseq:NGStraindata::NGStraindata">NGStraindata</a></code>. It was generated from <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>


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

train.mutationNum function

A data frame with 361 observations on the following 9 variables:
  <dl>
    <dt><code>T.sns</code></dt><dd>total count of SNSs/Mb</dd> <dt><code>S.sns</code></dt><dd>count of SNSs in simple sequence repeats/Mb</dd> <dt><code>T.ind</code></dt><dd>total count of indels/Mb</dd> <dt><code>S.ind</code></dt><dd>count of indels in simple sequence repeats/Mb</dd> <dt><code>T</code></dt><dd>total mutation count/Mb</dd> <dt><code>S</code></dt><dd>mutation count in simple sequence repeats/Mb</dd> <dt><code>ratio.sns</code></dt><dd>S.sns/T.sns</dd> <dt><code>ratio.ind</code></dt><dd>S.ind/T.ind</dd> <dt><code>ratio</code></dt><dd>S/T</dd> </dl> 

Format

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

train.mutationNum: Table of Mutation Numbers in Train Set Samples

Description

Usage

Arguments

Format

Source

Details