S4 classes

bcbioRNASeq-class

bcbio RNA-Seq data set

bcbioRNASeq()

bcbio RNA-Seq data set

coerce

Methods for coercing an object to a class

`[`(<bcbioRNASeq>,<ANY>,<ANY>,<ANY>)

Extract or replace parts of an object

show(<bcbioRNASeq>)

Show an object

updateObject(<bcbioRNASeq>)

Update an object to its current class definition

Counts

counts(<bcbioRNASeq>)

Counts

relativeLogExpression()

Relative log expression

slotAlignedCounts()

Slot aligned counts into object

tmm()

Trimmed mean of M-values

Plots

plot5Prime3PrimeBias()

Plot 5' to 3' bias

plotCorrelationHeatmap(<bcbioRNASeq>)

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

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()

Compare pseudoaligned counts to 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