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MSIseq (version 1.0.0)

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

Description

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.

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Version

Install

install.packages('MSIseq')

Monthly Downloads

14

Version

1.0.0

License

GPL (>= 2)

Maintainer

Mini Huang

Last Published

June 15th, 2015

Functions in MSIseq (1.0.0)

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

MSIseq.classify

Classify Microsatellite Instability with MSIseq Classifier

Mutation Annotation Data with Test Set Samples

Mutation Annotation Data with Training Set Samples

Compute.input.variables

Compute Mutation Counts from Tumor Exome Somatic Mutations

Build Microsatellite Instability Classification Model with Training Dataset

test.mutationNum

Table of Mutation Numbers in Test Set Samples

train.mutationNum

Table of Mutation Numbers in Train Set Samples

Read Fasta File

find.mono.repeats

Find Mono-nucleotide Repeats

Cancer Types for the TCGA Training Set Samples

Capture Sequence Length for Test Set Samples

MSI Status Classification for the TCGA Training Set Samples

Cancer Types for the TCGA Test Set Samples

Capture Sequence Length for Training Set Samples