ProteoDiscography: ProteoDiscography

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

ProteoDiscography

Description

An S4 object containing the reference genome sequences and gene-model annotations (TxDB).

This also stores genomic variants and splice-junctions from which mutant transcript sequences can be generated.

Slots

TxDb

(TxDb): TxDb object containing the genomic and transcript annotations.

genomeSeqs

(DNAStringSet or BSgenome): Genomic sequence of the respective genome.

input.genomicVariants

(VRangesList): Imported genomic variants (SNV, MNV and InDels).

input.spliceJunctions

(DataFrame): Imported splice-junctions.

input.manualSequences

(DataFrame): Imported manual sequences.

mutantTranscripts.genomicVariants

(tibble): Generated mutant mRNA sequences from genomic variants.

mutantTranscripts.spliceJunctions

(tibble): Generated mutant mRNA sequences from splice-junctions.

mutantTranscripts.manualSequences

(tibble): Processed mutant mRNA sequences from manual input.

GENETIC_CODE

(GENETIC_CODE_TABLE): The genetic code table to be used during translation.

metadata

(data.frame): Supplied data.frame.

Author(s)

Job van Riet

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