cleanUpdTSeq: This package classifies putative polyadenylation sites as true or false/internally oligodT primed
Version 1.14.0

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.

AuthorSarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Bioconductor views GeneRegulation Genetics SequenceMatching Sequencing
Date of publicationNone
MaintainerSarah Sheppard <Sarah.Sheppard@umassmed.edu>; Jianhong Ou <Jianhong.Ou@umassmed.edu>; Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
LicenseGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cleanUpdTSeq")

Getting started

Package overview
The cleanUpdTSeq user's guide

Popular man pages

buildClassifier: get Naive Bayes Classifier
cleanUpdTSeq-package: This package classifies putative polyadenylation sites.
data.NaiveBayes: Training Data
featureVector-class: Class '"featureVector"'
getUpstreamSequence: Get upstream sequences of the putative pA site
naiveBayes: Class '"naiveBayes"'
predictTestSet: predictTestSet
See all...

All man pages Function index File listing

Man pages

BED2GRangesSeq: BED2GRangesSeq
buildClassifier: get Naive Bayes Classifier
buildFeatureVector: buildFeatureVector
classifier: An object of class "naiveBayes" generated from...
cleanUpdTSeq-package: This package classifies putative polyadenylation sites.
data.NaiveBayes: Training Data
featureVector-class: Class '"featureVector"'
getDownstreamSequence: getDownstreamSequence
getUpstreamSequence: Get upstream sequences of the putative pA site
modelInfo-class: Class '"modelInfo"'
naiveBayes: Class '"naiveBayes"'
PASclassifier-class: Class '"PASclassifier"'
predictTestSet: predictTestSet

Functions

$,PASclassifier-method Man page
$,featureVector-method Man page
$,modelInfo-method Man page
$,naiveBayes-method Man page
$<-,PASclassifier-method Man page
$<-,featureVector-method Man page
$<-,modelInfo-method Man page
$<-,naiveBayes-method Man page
BED2GRangesSeq Man page Source code
PASclassifier Man page
PASclassifier-class Man page
buildClassifier Man page Source code
buildFeatureVector Man page Source code
classifier Man page
cleanUpdTSeq Man page
cleanUpdTSeq-package Man page
data.NaiveBayes Man page
featureVector Man page
featureVector-class Man page
getDownstreamSequence Man page Source code
getUpstreamSequence Man page Source code
modelInfo Man page
modelInfo-class Man page
naiveBayes Man page
naiveBayes-class Man page
predictTestSet Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/BED2GRangesSeq.R
R/buildClassifier.R
R/buildFeatureVector.R
R/getDownstreamSequence.R
R/getUpstreamSequence.R
R/predictTestSet.R
build
build/vignette.rds
data
data/classifier.rda
data/data.NaiveBayes.rda
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/cleanUpdTSeq.R
inst/doc/cleanUpdTSeq.Rmd
inst/doc/cleanUpdTSeq.html
inst/extdata
inst/extdata/test-predNaiveBayes.rds
inst/extdata/test-predNaiveBayes.xls
inst/extdata/test.bed
inst/unitTests
inst/unitTests/test_predictTestSet.R
man
man/BED2GRangesSeq.Rd
man/PASclassifier-class.Rd
man/buildClassifier.Rd
man/buildFeatureVector.Rd
man/classifier.Rd
man/cleanUpdTSeq-package.Rd
man/data.NaiveBayes.Rd
man/featureVector-class.Rd
man/getDownstreamSequence.Rd
man/getUpstreamSequence.Rd
man/modelInfo-class.Rd
man/naiveBayes.Rd
man/predictTestSet.Rd
tests
tests/runTests.R
vignettes
vignettes/cleanUpdTSeq.Rmd
cleanUpdTSeq documentation built on May 20, 2017, 10:53 p.m.

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