mapMutSig: Map mutations given a table of codons for each amino acid for...

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

Description

Map mutations given a table of codons for each amino acid for a given protein.

Usage

mapMutSig(
  prot_id,
  prot_length,
  mutMap,
  ensembldbObj,
  genomeObj,
  flank = 1,
  contexts = get32Contexts(),
  seqLevelStyle = "NCBI"
)

Arguments

prot_id	character, Ensembl protein ID
prot_length	integer, length (in amino acids) of the given protein
mutMap	data.frame list of mutations obtained from mapMut
ensembldbObj	Ensembl DB Object from the EnsDb package (see example)
genomeObj	Bioconductor genome object from which coding sequences are extracted (see example)
flank	integer, the number of flanking nucleotides with which to define mutational signatures. Only the value of 1 has been catered for at the moment. (Default: 1)
contexts	character vector, all possible DNA motifs on which mutational signatures are defined. Obtained from get32Contexts() (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 eight columns: chr: chromosome g_pos: genomic position AA_pos: integer, amino acid position of the given Ensembl protein WT_AA: wild-type amino acid (one-letter code) MUT_AA: mutant amino acid (one-letter code) WT_codon: codon corresponding to wild-type amino acid MUT_codon: codon corresponding to mutant amino acid MutSig: the corresponding mutational signature (96-contexts) corresponding to the given AA substitution

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")
codons_muts <- mapMut(codons, getPossibleMissenseSNVs())
codons_mutsigs <- mapMutSig(id, nrow(codons), codons_muts,
                            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.