assignMissingID {CAGEfightR} | R Documentation |
This function can relabel ranges with missing IDs (i.e. returned by assignTxID and assignGeneID), in case they need to be retained for further analysis.
assignMissingID(object, ...) ## S4 method for signature 'character' assignMissingID(object, prefix = "Novel") ## S4 method for signature 'GenomicRanges' assignMissingID(object, outputColumn = "geneID", prefix = "Novel") ## S4 method for signature 'RangedSummarizedExperiment' assignMissingID(object, outputColumn = "geneID", prefix = "Novel")
object |
character, GRanges or RangedSummarizedExperiment: IDs to have NAs replaces with new IDs. |
... |
additional arguments passed to methods. |
prefix |
character: New name to assign to ranges with missing IDs, in the style prefix1, prefix2, etc. |
outputColumn |
character: Name of column to hold txID values. |
object with NAs replaced in outputColumn
Other Annotation functions:
assignGeneID()
,
assignTxID()
,
assignTxType()
data(exampleUnidirectional) # Obtain gene models from a TxDb-object: library(TxDb.Mmusculus.UCSC.mm9.knownGene) txdb <- TxDb.Mmusculus.UCSC.mm9.knownGene # Assign geneIDs using only TC peaks: exampleUnidirectional <- assignGeneID(exampleUnidirectional, geneModels=txdb, outputColumn='geneID', swap='thick') # Replace NAs with 'Novel' assignMissingID(exampleUnidirectional) # Replace NAs with 'NovelTSS' assignMissingID(exampleUnidirectional, prefix = 'NovelTSS')