mutation-context: mutationContext functions
In SomaticSignatures: Somatic Signatures

Description Usage Arguments Details Value See Also Examples

Extract the sequence context surrounding SNVs from a genomic reference.

1 2	mutationContext(vr, ref, k = 3, strand = FALSE, unify = TRUE, check = FALSE) mutationContextMutect(vr, k = 3, unify = TRUE)

`vr`	'VRanges' with SNV substitutions, with 'ref' and 'alt' columns filled [required]. Each element of 'ref' and 'alt' have be a single base from the DNA bases (A,C,G,T). For 'mutationContextMutect', an object as returned by the 'readMutect' function.
`ref`	A 'BSgenome', 'FaFile' or 'TwoBitfile' object representing the reference sequence [required]. More generally, any object with a defined 'getSeq' method can be used.
`k`	The 'k'-mer size of the context, including the variant position [integer, default: 3]. The variant will be located at the middle of the k-mer which requires 'k' to be odd.
`strand`	Should all variants be converted to the 'plus' strand? [logical, default: FALSE].
`unify`	Should the alterations be converted to have a C/T base pair as a reference alleles? [logical, default: TRUE]
`check`	Should the reference base of 'vr' be checked against 'ref' [logical, default: TRUE]? In case the two references do not match, a warning will be printed.

The somatic motifs of a SNV, composed out of (a) the base change and (b) the sequence context surrounding the variant, is extracted from a genomic sequence with the 'mutationContext' function.

Different types of classes that represent the genomic sequence can used togther with the 'mutationContext' function: 'BSgenome', 'FastaFile' and 'TwoBitFile' objects are supported through Bioconductor by default. See the vignette for examples discussing an analysis with non-referene genomes.

For mutect variant calls, all relevant information is already contained in the results and somatic motifs can constructed by using the 'mutationContextMutect' function, without the need for the reference sequence.

The original 'VRanges' object 'vr', with the additional columns

`alteration`	DNAStringSet with 'ref\|alt'.
`context`	DNAStringSet with '..N..' of length 'k', where N denotes the variant position.

readMutect for mutationContextMutect

'showMethods("getSeq")' for genomic references that can be used

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  mutect_path = system.file("examples", "mutect.tsv", package = "SomaticSignatures")
  vr1 = readMutect(mutect_path)
  ct1 = mutationContextMutect(vr1)