S4 Class Definition

bcbioRNASeq()

bcbioRNASeq Object and Constructor

coerce

Methods for Coercing an Object to a Class

show(<bcbioRNASeq>)

Show an Object

updateObject(<bcbioRNASeq>)

Update Object

Data Functions

counts(<bcbioRNASeq>)

Count Matrix Accessors

metrics(<bcbioRNASeq>)

Sample Metrics

tmm()

Trimmed Mean of M-Values (TMM) Normalization

tpm()

Transcripts Per Million (TPM)

Plot Functions

plot5Prime3PrimeBias()

Plot 5'->3' Bias

plotCorrelationHeatmap(<bcbioRNASeq>) plotCorrelationHeatmap(<DESeqDataSet>)

Plot Correlation Heatmap

plotCountDensity()

Plot Count Density

plotCountsPerGene()

Plot Counts Per Gene

plotDEGHeatmap()

Differentially Expressed Gene Heatmap

plotDEGPCA()

Plot DEG PCA

plotDispEsts(<bcbioRNASeq>)

Plot Dispersion Estimates

plotExonicMappingRate()

Plot Exonic Mapping Rate

plotGenderMarkers()

Plot Sexually Dimorphic Gender Markers

plotGene(<SummarizedExperiment>) plotGene(<bcbioRNASeq>) plotGene(<DESeqDataSet>) plotGene(<DESeqTransform>)

Plot Individual Genes

plotGeneSaturation()

Plot Gene Detection Saturation

plotGenesDetected()

Plot Genes Detected

plotIntronicMappingRate()

Plot Intronic Mapping Rate

plotMappedReads()

Plot Mapped Reads

plotMappingRate()

Plot Mapping Rate

plotMeanAverage()

Plot Mean Average

plotMeanSD()

Plot Row Standard Deviations vs. Row Means

plotPCA(<SummarizedExperiment>) plotPCA(<DESeqDataSet>) plotPCA(<bcbioRNASeq>)

Sample PCA Plot for Transformed Data

plotPCACovariates()

Find Correlation Between Principal Components (PCs) and Covariates

plotRRNAMappingRate()

Plot Ribosomal RNA (rRNA) Mapping Rate

plotTotalReads()

Plot Total Reads

plotVolcano()

Plot Volcano

Differential Expression Functions

alphaSummary()

Alpha Level Cutoff Summary Statistics

contrastName()

Contrast Name

resultsTables()

Differential Expression Results Tables

topTables()

Top Tables of Differential Expression Results

R Markdown Functions

prepareRNASeqTemplate()

Prepare RNA-Seq R Markdown Template

Internal Data

genderMarkers

Gender Marker Genes

Example Data

GSE65267

bcb_small

bcbioRNASeq Example

dds_small

DESeqDataSet Example

res_small

DESeqResults Example

rld_small

DESeqTransform Example