R: Utility: Extract annotation hierachy from a TxDb.

utilsSimplifyTxDb {CAGEfightR}

R Documentation

Utility: Extract annotation hierachy from a TxDb.

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

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)