MSIseq: Assess Tumor Microsatellite Instability with a Decision Tree Classifier from Exome Somatic Mutations
Version 1.0.0

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.

AuthorMini Huang
Bioconductor views Classification Sequencing SomaticMutation
Date of publication2015-06-15 16:26:10
MaintainerMini Huang <mini.huang@nus.edu.sg>
LicenseGPL (>= 2)
Version1.0.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MSIseq")

Getting started

Package overview

Popular man pages

find.mono.repeats: Find Mono-nucleotide Repeats
MSIseq.classify: Classify Microsatellite Instability with MSIseq Classifier
MSIseq.train: Build Microsatellite Instability Classification Model with...
NGStestdata: Mutation Annotation Data with Test Set Samples
NGStestseqLen: Capture Sequence Length for Test Set Samples
NGStesttype: Cancer Types for the TCGA Test Set Samples
NGStrainclass: MSI Status Classification for the TCGA Training Set Samples
See all...

All man pages Function index File listing

Man pages

Compute.input.variables: Compute Mutation Counts from Tumor Exome Somatic Mutations
find.mono.repeats: Find Mono-nucleotide Repeats
MSIseq.classify: Classify Microsatellite Instability with MSIseq Classifier
MSIseq-package: Assess Tumor Microsatellite Instability with a Decision Tree...
MSIseq.train: Build Microsatellite Instability Classification Model with...
NGStestdata: Mutation Annotation Data with Test Set Samples
NGStestseqLen: Capture Sequence Length for Test Set Samples
NGStesttype: Cancer Types for the TCGA Test Set Samples
NGStrainclass: MSI Status Classification for the TCGA Training Set Samples
NGStraindata: Mutation Annotation Data with Training Set Samples
NGStrainseqLen: Capture Sequence Length for Training Set Samples
NGStraintype: Cancer Types for the TCGA Training Set Samples
read.fasta: Read Fasta File
test.mutationNum: Table of Mutation Numbers in Test Set Samples
train.mutationNum: Table of Mutation Numbers in Train Set Samples

Functions

Compute.input.variables Man page Source code
MSIseq Man page
MSIseq-package Man page
MSIseq.classify Man page Source code
MSIseq.train Man page Source code
NGStestdata Man page
NGStestseqLen Man page
NGStesttype Man page
NGStrainclass Man page
NGStraindata Man page
NGStrainseqLen Man page
NGStraintype Man page
find.mono.repeats Man page Source code
ntersects Source code
read.fasta Man page Source code
test.mutationNum Man page
train.mutationNum Man page

Files

inst
inst/doc
inst/doc/MSIseq.pdf
NAMESPACE
data
data/test.mutationNum.rda
data/NGStraindata.rda
data/NGStraintype.rda
data/train.mutationNum.rda
data/NGStesttype.rda
data/NGStrainclass.rda
data/NGStestdata.rda
data/datalist
data/NGStestseqLen.rda
data/NGStrainseqLen.rda
R
R/Compute.input.variables.R
R/MSIseq.train.R
R/sysdata.rda
R/find.mono.R
R/MSIseq.classify.R
vignettes
vignettes/MSIseq.Rnw
MD5
DESCRIPTION
man
man/find.mono.repeats.Rd
man/MSIseq.train.Rd
man/Compute.input.variables.Rd
man/read.fasta.Rd
man/NGStestdata.Rd
man/train.mutationNum.Rd
man/MSIseq.classify.Rd
man/test.mutationNum.Rd
man/NGStestseqLen.Rd
man/NGStraintype.Rd
man/NGStraindata.Rd
man/MSIseq-package.Rd
man/NGStesttype.Rd
man/NGStrainclass.Rd
man/NGStrainseqLen.Rd
MSIseq documentation built on May 19, 2017, 7:27 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.