trinucleotideMatrix {maftools} | R Documentation

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

### Description

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

### Usage

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

### Arguments

`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.

### Details

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.

### Value

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.

### References

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.

### See Also

`extractSignatures` `plotApobecDiff`

### Examples

    ## 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)

[Package maftools version 2.4.12 Index]