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.
|Date of publication||2015-06-15 16:26:10|
|Maintainer||Mini Huang <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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