exportProteoDiscography: Export the generated (mutant) peptides sequences to a FASTA...

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

Export the generated (mutant) peptides sequences to a FASTA database.

Description

Exports (mutant) peptide sequences to FASTA using several fields as identifier. In addition, users can specify to only export (mutant) sequences containing at a min. number of proteotypic fragments.

Usage

exportProteoDiscography(
  ProteoDiscography,
  outFile = NULL,
  minProteotypicFragments = NULL,
  aggregateSamples = TRUE
)

Arguments

ProteoDiscography	(ProteoDiscography): ProteoDiscography object which stores the annotation and genomic sequences.
outFile	(character): Filepath to output FASTA, will append the samplenames if aggregateSamples is FALSE. If left NULL, it will return an AAStringSet with the given records.
minProteotypicFragments	(integer): Only output mutant protein-isoforms from incorporated genomic variants with at least this many proteotypic fragments (if 'checkProteotypicFragments()' was performed).
aggregateSamples	(logical): Should samples be aggregated into the same output database (TRUE) or should a seperate FASTA-file be generated per sample (FALSE).

Value

Writes a FASTA file containing the mutant protein isoforms if outFile is given. Otherwise, will return an AAStringSet.

Author(s)

Job van Riet [e-mail]

Wesley van de Geer [e-mail]

Examples

# 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)

# Export peptide sequences to FASTA file. Optionally, only export those with at least a min.
# number of proteotypic fragments.
exportProteoDiscography(ProteoDiscographyExample.hg19, outFile = 'out.fasta')

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