cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data


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Documentation for package ‘cleanUpdTSeq’ version 1.30.0

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cleanUpdTSeq-package This package classifies putative polyadenylation sites.
$-method Class '"PASclassifier"'
$-method Class '"featureVector"'
$-method Class '"modelInfo"'
$-method Class '"naiveBayes"'
$<--method Class '"PASclassifier"'
$<--method Class '"featureVector"'
$<--method Class '"modelInfo"'
$<--method Class '"naiveBayes"'
BED6WithSeq2GRangesSeq Covert (extended) BED6 file to a GRanges object
buildClassifier Build a Naive Bayes Classifier
buildFeatureVector build Feature Vector_2
classifier NaiveBayes classifier
cleanUpdTSeq This package classifies putative polyadenylation sites.
data.NaiveBayes Training Data
featureVector Class '"featureVector"'
featureVector-class Class '"featureVector"'
getContextSequences Retrieve upstream and downstream sequences
modelInfo Class '"modelInfo"'
modelInfo-class Class '"modelInfo"'
naiveBayes Class '"naiveBayes"'
naiveBayes-class Class '"naiveBayes"'
PASclassifier Class '"PASclassifier"'
PASclassifier-class Class '"PASclassifier"'
predictTestSet predict authenticity of putative pA sites