importTranscriptSequences: Incorporate manual transcript sequences into the...

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

Incorporate manual transcript sequences into the ProteoDiscography

Description

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

• sample: Names of the samples. (character)

• identifier: The identifier which will be used in downstream analysis. (character)

• Tx.SequenceMut: The mutant mRNA sequence. (DNAStringSet)

• gene: Name of the gene. (character, optional)

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 [e-mail]

Wesley van de Geer [e-mail]

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
 )

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