assignTxType: Annotate ranges with transcript type.

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

Description

Annotate a set of ranges in a GRanges object with transcript type (txType) based on their genic context. Transcripts are obtained from a TxDb object, but can alternatively be specified manually as a GRangesList.

Usage

assignTxType(object, txModels, ...)

## S4 method for signature 'GenomicRanges,GenomicRangesList'
assignTxType(
  object,
  txModels,
  outputColumn = "txType",
  swap = NULL,
  noOverlap = "intergenic"
)

## S4 method for signature 'RangedSummarizedExperiment,GenomicRangesList'
assignTxType(object, txModels, ...)

## S4 method for signature 'GenomicRanges,TxDb'
assignTxType(
  object,
  txModels,
  outputColumn = "txType",
  swap = NULL,
  tssUpstream = 100,
  tssDownstream = 100,
  proximalUpstream = 1000,
  detailedAntisense = FALSE
)

## S4 method for signature 'RangedSummarizedExperiment,TxDb'
assignTxType(object, txModels, ...)

Arguments

object	GRanges or RangedSummarizedExperiment: Ranges to be annotated.
txModels	TxDb or GRangesList: Transcript models via a TxDb, or manually specified as a GRangesList.
...	additional arguments passed to methods.
outputColumn	character: Name of column to hold txType values.
swap	character or NULL: If not NULL, use another set of ranges contained in object to calculate overlaps, for example peaks in the thick column.
noOverlap	character: In case categories are manually supplied with as a GRangesList, what to call regions with no overlap.
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

object with txType added as factor column in rowData (or mcols)

See Also

Other Annotation functions: assignGeneID(), assignMissingID(), assignTxID()

Examples

## Not run: 
data(exampleUnidirectional)

# Obtain transcript models from a TxDb-object:
library(TxDb.Mmusculus.UCSC.mm9.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene

# Assign txIDs
assignTxType(exampleUnidirectional,
             txModels=txdb)

# Assign txIDs using only TC peaks:
exampleUnidirectional <- assignTxType(exampleUnidirectional,
                                      txModels=txdb,
                                      swap='thick')

# The 'promoter' and 'proximal' category boundaries can be changed:
assignTxType(exampleUnidirectional,
             txModels=txdb,
             swap='thick',
             tssUpstream=50,
             tssDownstream=50,
             proximalUpstream=100)

# Annotation using complete antisense categories:
exampleUnidirectional <- assignTxType(exampleUnidirectional,
                                    txModels=txdb,
                                    outputColumn='txTypeExtended',
                                    swap='thick',
                                    detailedAntisense=TRUE)

# The output is always a factor added as a column:
summary(rowRanges(exampleUnidirectional)$txType)
summary(rowRanges(exampleUnidirectional)$txTypeExtended)

# To avoid using a TxDb-object, a GRangesList can be supplied:
custom_hierarchy <- GRangesList(promoters=granges(promoters(txdb)),
                                exons=granges(exons(txdb)))
assignTxType(exampleUnidirectional,
             txModels=custom_hierarchy,
             outputColumn='customType',
             swap='thick',
             noOverlap = 'intergenic')

## End(Not run)

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.