trinucleotideMatrix: Extract single 5' and 3' bases flanking the mutated site for...
In maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Details Value References See Also Examples

Extract single 5' and 3' bases flanking the mutated site for de-novo signature analysis. Also estimates APOBEC enrichment scores.

trinucleotideMatrix(
  maf,
  ref_genome = NULL,
  prefix = NULL,
  add = TRUE,
  ignoreChr = NULL,
  useSyn = TRUE,
  fn = NULL
)

`maf`	an `MAF` object generated by `read.maf`
`ref_genome`	BSgenome object or name of the installed BSgenome package. Example: BSgenome.Hsapiens.UCSC.hg19 Default NULL, tries to auto-detect from installed genomes.
`prefix`	Prefix to add or remove from contig names in MAF file.
`add`	If prefix is used, default is to add prefix to contig names in MAF file. If false prefix will be removed from contig names.
`ignoreChr`	Chromsomes to ignore from analysis. e.g. chrM
`useSyn`	Logical. Whether to include synonymous variants in analysis. Defaults to TRUE
`fn`	If given writes APOBEC results to an output file with basename fn. Default NULL.

Extracts immediate 5' and 3' bases flanking the mutated site and classifies them into 96 substitution classes. Requires BSgenome data packages for sequence extraction.

APOBEC Enrichment: Enrichment score is calculated using the same method described by Roberts et al.

E = (n_tcw * background_c) / (n_C * background_tcw)

where, n_tcw = number of mutations within T[C>T]W and T[C>G]W context. (W -> A or T)

n_C = number of mutated C and G

background_C and background_tcw motifs are number of C and TCW motifs occuring around +/- 20bp of each mutation.

One-sided Fisher's Exact test is performed to determine the enrichment of APOBEC tcw mutations over background.

list of 2. A matrix of dimension nx96, where n is the number of samples in the MAF and a table describing APOBEC enrichment per sample.

Roberts SA, Lawrence MS, Klimczak LJ, et al. An APOBEC Cytidine Deaminase Mutagenesis Pattern is Widespread in Human Cancers. Nature genetics. 2013;45(9):970-976. doi:10.1038/ng.2702.

extractSignatures plotApobecDiff

## Not run: 
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19',
prefix = 'chr', add = TRUE, useSyn = TRUE)

## End(Not run)