S4 class for storing and manipulating expression data from assembled transcriptomes
tables containing expression data for genomic features (introns, exons, transcripts)
genomic locations of features and their relationships to one another
tables connecting components of the assembly and providing other experimental information (e.g., phenotype data and locations of read alignment files)
directories holding data created by
date the ballgown object was created
which expression measurement(s) the object contains in its data slot. Vector of one or more of "rcount", "ucount", "mrcount", "cov", "cov_sd", "mcov", "mcov_sd", or "FPKM", if Tablemaker output is used, or one of "TPM" or "FPKM" if RSEM output is used. Can also be "all" for all measurements. See vignette for details.
TRUE if object was made from RSEM output, FALSE if object was made from Tablemaker/Cufflinks output.
Alyssa Frazee, Leonardo Collado Torres, Jeff Leek
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