utilsSimplifyTxDb: Utility: Extract annotation hierachy from a TxDb.

In CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Description

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.

Usage

utilsSimplifyTxDb(
  object,
  tssUpstream = 100,
  tssDownstream = 100,
  proximalUpstream = 1000,
  detailedAntisense = FALSE
)

Arguments

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).

Value

GRangesList of annotation hierachy

See Also

assignTxType

Other Utility functions: utilsAggregateRows(), utilsDeStrand(), utilsScoreOverlaps()

Examples

## 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)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.