NGStrainclass


This is a data frame containing the MSI status for each sample in <code><a rd-options="MSIseq:train.mutationNum" href="/link/train.mutationNum?package=MSIseq&version=1.0.0&to=MSIseq%3Atrain.mutationNum" data-mini-rdoc="MSIseq:train.mutationNum::train.mutationNum">train.mutationNum</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

NGStrainclass function

A data frame with 426 observations on the following 2 variables:
  <dl>
    <dt><code>Tumor_Sample_Barcode</code></dt><dd>the sample ID as a character vector</dd> <dt><code>MSI_status</code></dt><dd>a factor indicating MSI status for each sample, containing two levels: "MSI-H" and "Non-MSI-H". Other values will cause <code><a rd-options="MSIseq:MSIseq.train" href="/link/MSIseq.train?package=MSIseq&version=1.0.0&to=MSIseq%3AMSIseq.train" data-mini-rdoc="MSIseq:MSIseq.train::MSIseq.train">MSIseq.train</a></code> to generate an error.</dd> </dl> 

Format

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

NGStrainclass: MSI Status Classification for the TCGA Training Set Samples

Description

Usage

Arguments

Format

Source

Details