importTranscriptSequences {ProteoDisco}R Documentation

Incorporate manual transcript sequences into the ProteoDiscography

Description

The given DataFrame (transcripts) should include the following columns:

The supplied mutant sequences do not need to have a respective record within the used TxDb as these are handled as independent sequences.

Usage

importTranscriptSequences(
  ProteoDiscography,
  transcripts,
  removeExisting = FALSE,
  overwriteDuplicateSamples = FALSE
)

Arguments

ProteoDiscography

(ProteoDiscography): ProteoDiscography object which stores the annotation and genomic sequences.

transcripts

(DataFrame): DataFrame containing metadata and the transcript sequences.

removeExisting

(logical): Should previous mutations within the ProteoDiscography be removed?

overwriteDuplicateSamples

(logical): Replace duplicate samples (TRUE) or throw an error if duplicate samples are found.

Value

ProteoDiscography with added mutant transcript sequences from manual input.

Author(s)

Job van Riet j.vanriet@erasmusmc.nl

Wesley van de Geer w.vandegeer@erasmusmc.nl

Examples


 ProteoDiscography.hg19 <- ProteoDisco::generateProteoDiscography(
   TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, 
   genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
 )
 
 manualSeq <- S4Vectors::DataFrame(
   sample = rep('Example', 2),
   identifier = c('Example 1', 'Example 2'),
   gene = c('GeneA', 'GeneB'),
   Tx.SequenceMut = Biostrings::DNAStringSet(list(Biostrings::DNAString('ATCGGGCCCGACGTT'), Biostrings::DNAString('GCTAGCGATCAGGGA')))
 )

 # Add to ProteoDiscography.
 ProteoDiscography.hg19 <- ProteoDisco::importTranscriptSequences(
   ProteoDiscography.hg19, 
   transcripts = manualSeq
 )


[Package ProteoDisco version 0.99.12 Index]