Differential Analysis of Translation Efficiency and Usage of Open Reading Frames

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Documentation for package ‘DOTSeq’ version 0.99.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

DOTSeq-package	DOTSeq: Differential Analysis of Translation Efficiency and Usage of Open Reading Frames
.PostHoc	The PostHoc class for DOTSeq
calculateUsage	Calculate ORF usage across conditions from a SummarizedExperiment
countReads	Count reads from BAM files over genomic features
DOTSeq	DOTSeq: Differential Analysis of Translation Efficiency and Usage of Open Reading Frames
DOTSeqDataSets-class	DOTSeqDataSets-class
DOTSeqDataSetsFromFeatureCounts	Construct DOTSeqDatasets from featureCounts output for Differential ORF Translation Analysis
DOTSeqDataSetsFromSummarizeOverlaps	Construct DOTSeqDatasets from featureCounts output for Differential ORF Translation Analysis
DOUData-class	DOUData-class
DOUData-validity	Validity method for DOUData
DTEData-class	DTEData-class
findORFsFasta	Find ORFs in FASTA sequences using ORFik's C++ engine
fitDOU	Fit Differential ORF Usage Models
fitResults	Access the model type from a PostHoc object
fitResults-method	Access the model type from a PostHoc object
getContrasts	Access and replace contrast results from post hoc analysis
getContrasts-method	Access and replace contrast results from post hoc analysis
getContrasts<-	Access and replace contrast results from post hoc analysis
getContrasts<--method	Access and replace contrast results from post hoc analysis
getDOU	Accessor and replacement methods for DOU slot
getDOU-method	Accessor and replacement methods for DOU slot
getDOU<-	Accessor and replacement methods for DOU slot
getDOU<--method	Accessor and replacement methods for DOU slot
getDTE	Accessor and replacement methods for DTE slot
getDTE-method	Accessor and replacement methods for DTE slot
getDTE<-	Accessor and replacement methods for DTE slot
getDTE<--method	Accessor and replacement methods for DTE slot
getExonicReads	Filter BAM files to retain only reads overlapping exonic regions
getORFs	Extract Genomic ORFs from Transcript Sequences
mapIDs	Retrieve Gene Symbols from Ensembl or Ensembl Genomes
modelType	Access the model type from a PostHoc object
modelType-method	Access the model type from a PostHoc object
numExonsPerGroup	Get list of the number of exons per group
plotDOT	Generate Differential ORF Translation (DOT) Visualization Suite
PostHoc	Construct a PostHoc Object
posthoc	Access the model type from a PostHoc object
PostHoc-class	The PostHoc class for DOTSeq
posthoc-method	Access the model type from a PostHoc object
remove_random_effects	Remove random effects from a formula
show-method	DOTSeqDataSets-class
simDOT	Simulate Differential ORF Translation (DOT)
testDOU	Compute Differential ORF Usage (DOU) Contrasts Using EMMs