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S4 classes

bcbioRNASeq-class
bcbio RNA-Seq data set
bcbioRNASeq()
bcbio RNA-Seq data set
as.DESeqDataSet() as.DESeqTransform() as.DGEList()
Methods for coercing an object to a class
`[`(<bcbioRNASeq>,<ANY>,<ANY>,<ANY>)
Extract or replace parts of an object
show()
Show an object
updateObject()
Update object

Counts

counts() `counts<-`()
Counts
relativeLogExpression()
Relative log expression
slotAlignedCounts()
Slot aligned counts
tmm()
Trimmed mean of M-values

Plots

plot5Prime3PrimeBias()
Plot 5' to 3' bias
plotCorrelationHeatmap()
Correlation heatmap
plotCounts()
Plot counts
plotCountsPerBiotype() plotCountsPerBroadClass()
Plot counts per biotype
plotCountsPerFeature() plotCountsPerGene() plotCountDensity()
Plot counts per feature
plotDispEsts()
Plot dispersion estimates
plotExonicMappingRate()
Plot exonic mapping rate
plotGenderMarkers()
Plot sexually dimorphic gender marker genes
plotGeneSaturation()
Plot gene detection saturation
plotIntronicMappingRate()
Plot intronic mapping rate
plotMappedReads()
Plot mapped reads
plotMappingRate()
Plot mapping rate
plotMeanSD()
Plot row standard deviations vs. row means
plotPCA()
Principal component analysis plot
plotPCACovariates()
Find correlation between principal components (PCs) and covariates
plotPseudoVsAlignedCounts()
Plot pseudo vs. aligned counts
plotQC()
Quality control
plotRRNAMappingRate()
Plot ribosomal RNA (rRNA) mapping rate
plotTotalReads()
Plot total reads

Example data

bcb
bcbio RNA-seq example data set

Reexports

reexports
Objects exported from other packages