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

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.

Author
Sarah Sheppard, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu
Date of publication
None
Maintainer
Sarah Sheppard <Sarah.Sheppard@umassmed.edu>; Jianhong Ou <Jianhong.Ou@umassmed.edu>; Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
License
GPL-2
Version
1.12.0

View on Bioconductor

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

Files in this package

cleanUpdTSeq/DESCRIPTION
cleanUpdTSeq/NAMESPACE
cleanUpdTSeq/NEWS
cleanUpdTSeq/R
cleanUpdTSeq/R/AllClasses.R
cleanUpdTSeq/R/BED2GRangesSeq.R
cleanUpdTSeq/R/buildClassifier.R
cleanUpdTSeq/R/buildFeatureVector.R
cleanUpdTSeq/R/getDownstreamSequence.R
cleanUpdTSeq/R/getUpstreamSequence.R
cleanUpdTSeq/R/predictTestSet.R
cleanUpdTSeq/build
cleanUpdTSeq/build/vignette.rds
cleanUpdTSeq/data
cleanUpdTSeq/data/classifier.rda
cleanUpdTSeq/data/data.NaiveBayes.rda
cleanUpdTSeq/data/datalist
cleanUpdTSeq/inst
cleanUpdTSeq/inst/CITATION
cleanUpdTSeq/inst/doc
cleanUpdTSeq/inst/doc/cleanUpdTSeq.R
cleanUpdTSeq/inst/doc/cleanUpdTSeq.Rmd
cleanUpdTSeq/inst/doc/cleanUpdTSeq.html
cleanUpdTSeq/inst/extdata
cleanUpdTSeq/inst/extdata/test-predNaiveBayes.rds
cleanUpdTSeq/inst/extdata/test-predNaiveBayes.xls
cleanUpdTSeq/inst/extdata/test.bed
cleanUpdTSeq/inst/unitTests
cleanUpdTSeq/inst/unitTests/test_predictTestSet.R
cleanUpdTSeq/man
cleanUpdTSeq/man/BED2GRangesSeq.Rd
cleanUpdTSeq/man/PASclassifier-class.Rd
cleanUpdTSeq/man/buildClassifier.Rd
cleanUpdTSeq/man/buildFeatureVector.Rd
cleanUpdTSeq/man/classifier.Rd
cleanUpdTSeq/man/cleanUpdTSeq-package.Rd
cleanUpdTSeq/man/data.NaiveBayes.Rd
cleanUpdTSeq/man/featureVector-class.Rd
cleanUpdTSeq/man/getDownstreamSequence.Rd
cleanUpdTSeq/man/getUpstreamSequence.Rd
cleanUpdTSeq/man/modelInfo-class.Rd
cleanUpdTSeq/man/naiveBayes.Rd
cleanUpdTSeq/man/predictTestSet.Rd
cleanUpdTSeq/tests
cleanUpdTSeq/tests/runTests.R
cleanUpdTSeq/vignettes
cleanUpdTSeq/vignettes/cleanUpdTSeq.Rmd