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

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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.

Author
Mini Huang
Date of publication
2015-06-15 16:26:10
Maintainer
Mini Huang <mini.huang@nus.edu.sg>
License
GPL (>= 2)
Version
1.0.0

View on CRAN

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

Files in this package

MSIseq
MSIseq/inst
MSIseq/inst/doc
MSIseq/inst/doc/MSIseq.pdf
MSIseq/NAMESPACE
MSIseq/data
MSIseq/data/test.mutationNum.rda
MSIseq/data/NGStraindata.rda
MSIseq/data/NGStraintype.rda
MSIseq/data/train.mutationNum.rda
MSIseq/data/NGStesttype.rda
MSIseq/data/NGStrainclass.rda
MSIseq/data/NGStestdata.rda
MSIseq/data/datalist
MSIseq/data/NGStestseqLen.rda
MSIseq/data/NGStrainseqLen.rda
MSIseq/R
MSIseq/R/Compute.input.variables.R
MSIseq/R/MSIseq.train.R
MSIseq/R/sysdata.rda
MSIseq/R/find.mono.R
MSIseq/R/MSIseq.classify.R
MSIseq/vignettes
MSIseq/vignettes/MSIseq.Rnw
MSIseq/MD5
MSIseq/DESCRIPTION
MSIseq/man
MSIseq/man/find.mono.repeats.Rd
MSIseq/man/MSIseq.train.Rd
MSIseq/man/Compute.input.variables.Rd
MSIseq/man/read.fasta.Rd
MSIseq/man/NGStestdata.Rd
MSIseq/man/train.mutationNum.Rd
MSIseq/man/MSIseq.classify.Rd
MSIseq/man/test.mutationNum.Rd
MSIseq/man/NGStestseqLen.Rd
MSIseq/man/NGStraintype.Rd
MSIseq/man/NGStraindata.Rd
MSIseq/man/MSIseq-package.Rd
MSIseq/man/NGStesttype.Rd
MSIseq/man/NGStrainclass.Rd
MSIseq/man/NGStrainseqLen.Rd