annotate_assembly       match assembled transcripts to annotated
                        transcripts
ballgown-class          Ballgown
ballgown-constructor    constructor function for ballgown objects
ballgown-package        The ballgown package for analysis of transcript
                        assemblies
ballgownrsem            load RSEM data into a ballgown object
bg                      Toy ballgown object
checkAssembledTx        plot annotated and assembled transcripts
                        together
clusterTranscripts      group a gene's assembled transcripts into
                        clusters
collapseTranscripts     cluster a gene's transcripts and calculate
                        cluster-level expression
contains                determine if one set of GRanges fully contains
                        any of another set of GRanges
dirs                    extract paths to tablemaker output
eexpr                   extract exon-level expression measurements from
                        ballgown objects
expr                    extract expression components from ballgown
                        objects
expr<-                  Replacement method for expr slot in ballgown
                        objects
exprfilter              subset ballgown objects using an expression
                        filter
geneIDs                 get gene IDs from a ballgown object
geneNames               get gene names from a ballgown object
getAttributeField       extract a specific field of the "attributes"
                        column of a data frame created from a GTF/GFF
                        file
getGenes                label assembled transcripts with gene names
gexpr                   extract gene-level expression measurements from
                        ballgown objects
gffRead                 read in GTF/GFF file as a data frame
gffReadGR               read in gtf file as GRanges object
iexpr                   extract transcript-level expression
                        measurements from ballgown objects
indexes                 extract the indexes from ballgown objects
indexes<-               Replace method for indexes slot in ballgown
                        objects
last                    get the last element
mergedDate              extract package version & creation date from
                        ballgown object
pData                   extract phenotype data from a ballgown object
pData<-                 Replacement method for pData slot in ballgown
                        objects
pctOverlap              calculate percent overlap between two GRanges
                        objects
plotLatentTranscripts   cluster assembled transcripts and plot the
                        results
plotMeans               visualize transcript abundance by group
plotTranscripts         visualize structure of assembled transcripts
sampleNames             get names of samples in a ballgown objects
seqnames                get sequence (chromosome) names from ballgown
                        object
stattest                statistical tests for differential expression
                        in ballgown
structure               extract structure components from ballgown
                        objects
subset                  subset ballgown objects to specific samples or
                        genomic locations
tGene                   Connect a transcript to its gene
texpr                   extract transcript-level expression
                        measurements from ballgown objects
transcriptIDs           get numeric transcript IDs from a ballgown
                        object
transcriptNames         get transcript names from a ballgown object
writeFiles              write files to disk from ballgown object
