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cleanUpdTSeq (version 1.10.2)

This package classifies putative polyadenylation sites as true or false/internally oligodT primed

Description

This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.

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Version

Version

1.10.2

License

GPL-2

Maintainer

Sarah Sheppard

Last Published

February 15th, 2017

Functions in cleanUpdTSeq (1.10.2)

PASclassifier-class

Class "PASclassifier"
data.NaiveBayes

Training Data
predictTestSet

predictTestSet
modelInfo-class

Class "modelInfo"
buildFeatureVector

buildFeatureVector
classifier

An object of class "naiveBayes" generated from data.NaiveBayes
getDownstreamSequence

getDownstreamSequence
naiveBayes-class

Class "naiveBayes"
buildClassifier

get Naive Bayes Classifier
getUpstreamSequence

Get upstream sequences of the putative pA site
BED2GRangesSeq

BED2GRangesSeq
featureVector-class

Class "featureVector"
cleanUpdTSeq-package

This package classifies putative polyadenylation sites.