utilsSimplifyTxDb {CAGEfightR} | R Documentation |
Used by assignTxType. This function extracts the hierachical annotations used by assignTxType from a TxDb object. If you are annotating many ranges, it can be time saving to built the hierachy first, to avoid processing the TxDb for every assignTxDb call.
utilsSimplifyTxDb( object, tssUpstream = 100, tssDownstream = 100, proximalUpstream = 1000, detailedAntisense = FALSE )
object |
TxDb: Transcript database |
tssUpstream |
integer: Distance to extend annotated promoter upstream. |
tssDownstream |
integer: Distance to extend annotated promoter downstream. |
proximalUpstream |
integer: Maximum distance upstream of promoter to be considered proximal. |
detailedAntisense |
logical: Wether to mirror all txType categories in the antisense direction (TRUE) or lump them all together (FALSE). |
GRangesList of annotation hierachy
assignTxType
Other Utility functions:
utilsAggregateRows()
,
utilsDeStrand()
,
utilsScoreOverlaps()
## Not run: data(exampleUnidirectional) # Obtain transcript models from a TxDb-object: library(TxDb.Mmusculus.UCSC.mm9.knownGene) txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene # Simplify txdb hierachy <- utilsSimplifyTxDb(txdb) # Standard way of calling x <- assignTxType(exampleUnidirectional, txModels=txdb) # Calling with premade hierachy y <- assignTxType(exampleUnidirectional, txModels=hierachy) # These are identical stopifnot(all(rowRanges(x)$txType == rowRanges(y)$txType)) ## End(Not run)