assignTxType {CAGEfightR} | R Documentation |
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.
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, ...)
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). |
object with txType added as factor column in rowData (or mcols)
Other Annotation functions:
assignGeneID()
,
assignMissingID()
,
assignTxID()
## 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)