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This function converts an object of data.frame from a bed file with sequence information to GRanges with sequence information.
● Data Source:
BioConductor
● Keywords: misc
● Alias: BED2GRangesSeq
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An object of class "PASclassifier" represents the output of buildClassifier
● Data Source:
BioConductor
● Keywords: classes
● Alias: $,PASclassifier-method, $<-,PASclassifier-method, PASclassifier, PASclassifier-class
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Computes the conditional a-posterior probabilities of a categorical class variable given independent predictor variables using the Bayes rule.
● Data Source:
BioConductor
● Keywords: misc
● Alias: buildClassifier
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This function creates a data frame. Fields include peak name, upstream sequence, downstream sequence, and features to be used in classifying the putative polyadenylation site.
● Data Source:
BioConductor
● Keywords: misc
● Alias: buildFeatureVector
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3'ends of transcripts have generally been poorly annotated. With the advent of deep sequencing, many methods have been developed to identify 3'ends. The majority of these methods use an oligodT primer which can bind to internal adenine-rich sequences, and lead to artifactual identification of polyadenylation sites. Heuristic filtering methods rely on a certain number of As downstream of a putative polyadenylation site to classify the site as true or oligodT primed. This package provides a robust method to classify putative polyadenylation sites using a Naive Bayes classifier.
● Data Source:
BioConductor
● Keywords: package
● Alias: cleanUpdTSeq, cleanUpdTSeq-package
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An object of class "featureVector" represents the output of buildFeatureVector
● Data Source:
BioConductor
● Keywords: classes
● Alias: $,featureVector-method, $<-,featureVector-method, featureVector, featureVector-class
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This function gets the sequence upstream of a putative pA site (including the site)
● Data Source:
BioConductor
● Keywords: misc
● Alias: getDownstreamSequence
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This function gets the sequence upstream of a putative pA site (including the site)
● Data Source:
BioConductor
● Keywords: misc
● Alias: getUpstreamSequence
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An object of class "modelInfo" represents the information of sequence to use in the analysis
● Data Source:
BioConductor
● Keywords: classes
● Alias: $,modelInfo-method, $<-,modelInfo-method, modelInfo, modelInfo-class
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An object of class "naiveBayes" represents the conditional a-posterior probabilities of a categorical class variable given independent predictor variables using the Bayes rule.
● Data Source:
BioConductor
● Keywords: classes
● Alias: $,naiveBayes-method, $<-,naiveBayes-method, naiveBayes, naiveBayes-class
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providing 
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