# Flexible, isoform-level differential expression analysis

## Documentation for package ‘ballgown’ version 2.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ballgown-package | The ballgown package for analysis of transcript assemblies
annotate_assembly | match assembled transcripts to annotated transcripts
Ballgown | Ballgown
ballgown | constructor function for ballgown objects
ballgown-class | Ballgown
ballgown-constructor | constructor function for ballgown objects
ballgownp | 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
dirs-method | extract paths to tablemaker output
eexpr | extract exon-level expression measurements from ballgown objects
eexpr-method | extract exon-level expression measurements from ballgown objects
expr | extract expression components from ballgown objects
expr-method | extract expression components from ballgown objects
expr<- | Replacement method for expr slot in ballgown objects
expr<--method | Replacement method for expr slot in ballgown objects
exprfilter | subset ballgown objects using an expression filter
geneIDs | get gene IDs from a ballgown object
geneIDs-method | get gene IDs from a ballgown object
geneNames | get gene names from a ballgown object
geneNames-method | 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
gexpr-method | 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
iexpr-method | extract transcript-level expression measurements from ballgown objects
indexes | extract the indexes from ballgown objects
indexes-method | extract the indexes from ballgown objects
indexes<- | Replace method for indexes slot in ballgown objects
indexes<--method | Replace method for indexes slot in ballgown objects
last | get the last element
mergedDate | extract package version & creation date from ballgown object
mergedDate-method | extract package version & creation date from ballgown object
pctOverlap | calculate percent overlap between two GRanges objects
pData | extract phenotype data from a ballgown object
pData-method | extract phenotype data from a ballgown object
pData<- | Replacement method for pData slot in ballgown objects
pData<--method | Replacement method for pData slot in ballgown 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
sampleNames-method | get names of samples in a ballgown objects
seqnames | get sequence (chromosome) names from ballgown object
seqnames-method | get sequence (chromosome) names from ballgown object
stattest | statistical tests for differential expression in ballgown
structure | extract structure components from ballgown objects
structure-method | extract structure components from ballgown objects
subset | subset ballgown objects to specific samples or genomic locations
subset-method | subset ballgown objects to specific samples or genomic locations
texpr | extract transcript-level expression measurements from ballgown objects
texpr-method | extract transcript-level expression measurements from ballgown objects
tGene | find the gene to which a transcript belongs
transcriptIDs | get numeric transcript IDs from a ballgown object
transcriptIDs-method | get numeric transcript IDs from a ballgown object
transcriptNames | get transcript names from a ballgown object
transcriptNames-method | get transcript names from a ballgown object
writeFiles | write files to disk from ballgown object