mutationPatterns: Mutation patterns of mutators

In AlexJanse/cMut: Identify Clustered Single Nucleotide Mutations and Link Them to Mutational Patterns

Description

A small data set of mutationpatterns of known mutators in human DNA. If you're using this as a reference to build a searchPattern table, then be sure to include the * marked columns. The ** marked columns means that at least one of the two is needed. Hereby is the data itself important and not necessary the header name. As seen in the table, there are two kinds of patterns:

• Patterns with 1 reference, 1 alternative, with surrounding nucleotides and a maximum distance with a number or NA. These are used in the identifyClusters and linkPatterns functions. These patterns will be called mutation patterns in the documentation of this package.

• Patterns with more than 1 or no reference, more than 1 alternative, no surrounding nucleotides and always a maximum distance. These are used in the groupClusters function. These are separated evaluated from the other patterns because these patterns depend on the order and distance of the mutations within a cluster. These patterns will be called cluster patterns in the documentation of this package.

For both pattern types it is possible to use DNA symbols. See dnaAlphabet for more information.

Usage

mutationPatterns

Format

A data frame with 15 rows and 5 columns

process

*A process that is connected with the mutation pattern.

ref

*Nucleotide that is found in the reference genome.

alt

*Nucleotide that is observed instead of the reference nucleotide.

surrounding

**The surrounding nucleotides where the mutation takes place. The "." represent the location of the mutation. The symbol itself can be anything as long as it's adjusted correctly when using functions that ask for the searchMutationSymbol.

maxDistance

**The maximum distance to the next mutation within a cluster. See the table to see where NA's are allowed and where not.

reference

A column with the reference of the process and it's mutation pattern.

AlexJanse/cMut documentation built on May 25, 2019, 4 a.m.