mapCodon: Map codons for each amino acid for a given protein.

In josef0731/CDSMutSig: Mapping Coding Sequences between DNA Mutational signatures and Amino Acid Changes

Description

Map codons for each amino acid for a given protein.

Usage

mapCodon(prot_id, ensembldbObj, genomeObj, seqLevelStyle = "NCBI")

Arguments

prot_id	character, Ensembl protein ID
ensembldbObj	Ensembl DB Object from the EnsDb package (see example)
genomeObj	Bioconductor genome object from which coding sequences are extracted (see example)
seqLevelStyle	Either "UCSC" or "NCBI". Denote conventions used in genome object to name chromosomes. Need changing to match the genome object. (Default: "NCBI")

Value

A data.frame with four columns: AA_pos: integer, amino acid position of the given Ensembl protein AA: amino acid (one-letter code) codon: codon corresponding to AA exon: the exon(s) in which the given AA can be found. Amino acids which span across exons are denoted as a semicolon-separated triplets of exon IDs, with each entry corresponding to each position of the codon.

Examples

require(EnsDb.Hsapiens.v75)
require(BSgenome.Hsapiens.UCSC.hg19)
id <- "ENSP00000233146"
codons <- mapCodon(id, EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75,
                   BSgenome.Hsapiens.UCSC.hg19::Hsapiens,
                   seqLevelStyle = "UCSC")

josef0731/CDSMutSig documentation built on Dec. 21, 2021, 2:19 a.m.