factRObject-class.RdA container for storing and processing custom transcriptome.
The factRObject is a representation of custom-assembled transcriptome data. Coordinate and metadata information from an input transcriptome (GTF) is parsed and grouped into 3 data Sets which corresponds to the levels of gene (genes), transcript (txs) and alternative splicing (ase). With the aid of a compatible reference genome and expression data, functional and comparative analyses can be performed to better understand the complexity of a transcriptome.
createfactRObject(gtf, reference)
Interact with a factRObject (x) the following ways:
summary(x): Prints preview of factRObject
head(x): Prints the first 6 metadata entries of the active Set
tail(x): Prints the last 6 metadata entries of the active Set
dim(x): Prints the dimension of the active set (features x samples)
nrow(x): Returns the number of features of the active set
ncol(x): Returns the number of samples
A factRObject consists of 3 `Sets` of data: gene, transcript and AS. At any one time, one of these `Sets` will be made the active Set and some factR2 functions will be called only on this active Set. Below are some ways to check and change the active Set:
listSets(x): Lists Sets in object
activeSet(x): Returns the active Set of object
activeSet(x)<-: Change the active Set
Each `Set` of an factRObject hold rich information of the features that it contains. Below are some convenient wrappers to display the metadata in each `Set`.
features(x): Displays metadata of active Set
genes(x) or gns(x): Displays gene metadata
transcripts(x) or txs(x): Displays transcript metadata
ase(x): Displays alternative splicing events metadata
factR2 also contain functions to plot exon-level and domain-level structures as an interactive plot:
plotTranscripts(x, "gene of interest"): Plots transcripts
plotDomains(x, "gene of interest")): Plots domains
If transcript-level counts data is provided, additional accessors are available: