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