setMutantTranscripts: Adds mutant transcript sequences to the ProteoDiscography in...

In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

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'
)

ErasmusMC-CCBC/ProteoDisco documentation built on Dec. 9, 2022, 8:41 a.m.