Function reference • bcbioRNASeq

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() plotCountDensity(): Plot counts per feature

plotDispEsts(): Plot dispersion estimates

plotExonicMappingRate(): Plot exonic mapping rate

plotFeatureSaturation(): Plot feature (gene) detection saturation

plotGenderMarkers(): Plot sexually dimorphic gender marker genes

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 alphaSummary loadRemoteData plotFeaturesDetected plotHeatmap plotQuantileHeatmap saveData: Objects exported from other packages