setMutantTranscripts {ProteoDisco}R Documentation

Adds mutant transcript sequences to the ProteoDiscography in the appropriate slot

Description

Adds mutant transcript sequences to the ProteoDiscography in the appropriate slot

Usage

setMutantTranscripts(x, transcripts, slotType)

## S4 method for signature 'ProteoDiscography'
setMutantTranscripts(x, transcripts, slotType)

## S4 method for signature 'ProteoDiscography'
mutantTranscripts(x)

Arguments

x

(ProteoDiscography): The ProteoDiscography for which the slot will be edited.

transcripts

(DataFrame): Transcripts to be used in the slot.

slotType

(character): Implemented slot to be edited.

Value

ProteoDiscography with updated records.

Examples


# From a ProteoDiscography with imported and incorporated records, take only the first 10 records.
# ProteoDisco::setMutantTranscripts(ProteoDiscography)$genomicVariants[1:10], slotType = 'genomicVariants')
# ProteoDisco::setMutantTranscripts(ProteoDiscography)$spliceJunctions[1:10], slotType = 'spliceJunctions')
# ProteoDisco::setMutantTranscripts(ProteoDiscography)$manualSequences[1:10], slotType = 'manualSequences')

# Import example ProteoDiscography (hg19)
data('ProteoDiscographyExample.hg19', package = 'ProteoDisco')
ProteoDiscographyExample.hg19 <- setTxDb(ProteoDiscographyExample.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene)
ProteoDiscographyExample.hg19 <- setGenomicSequences(ProteoDiscographyExample.hg19, BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)

# Only keep the first ten records.
ProteoDiscographyExample.hg19 <- ProteoDisco::setMutantTranscripts(
  x = ProteoDiscographyExample.hg19,
  transcripts = ProteoDisco::mutantTranscripts(ProteoDiscographyExample.hg19)$genomicVariants[1:10,],
  slotType = 'genomicVariants'
)


[Package ProteoDisco version 1.0.0 Index]