All functions

assertFormalAnnotationCol()

Assert Formal Annotation Column

assertFormalInterestingGroups()

Interesting Groups Formal Assert Check

bcbioBase-package

bcbioBase

coerce

Methods for Coercing an Object to a Class

convertGenesToSymbols(<SummarizedExperiment>)

Convert Genes to Symbols

copyToDropbox()

Copy Files to Dropbox

counts(<SummarizedExperiment>)

Counts

flatFiles()

Flat Files from S4 Object

gene2symbol()

Gene to Symbol Mappings

bcbio_geom_abline() bcbio_geom_label() bcbio_geom_label_average() bcbio_geom_label_repel()

ggplot2 Functions

interestingGroups() `interestingGroups<-`()

Interesting Groups

plotCorrelationHeatmap()

Plot Correlation Heatmap

plotHeatmap()

Plot Heatmap

plotQuantileHeatmap()

Plot Heatmap with Quantile Breaks

prepareSummarizedExperiment()

Prepare Summarized Experiment

prepareTemplate()

Prepare R Markdown Template File

readDataVersions()

Read Data Versions

readLog()

Read Log File

readProgramVersions()

Read Program Versions

readSampleData()

Read Sample Metadata

readTx2gene()

Transcript to Gene Annotations

readYAMLSampleData() readYAMLSampleMetrics()

Read YAML Sample Data and Metrics

rse_bcb

RangedSummarizedExperiment Coerced from bcbioRNASeq

rse_dds

RangedSummarizedExperiment Coerced from DESeqDataSet

sampleData() `sampleData<-`() sampleNames(<SummarizedExperiment>)

Sample Data

sampleDirs()

Sample Directories

sampleNames

Sample Names

sanitizeSampleData()

Sanitize Sample Data

selectSamples()

Select Samples

uniteInterestingGroups()

Unite Interesting Groups