addLinkPatterns: addLinkPatterns

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

Description

A function to add columns to the sent table with information gathered from the linkPatterns function.

Usage

addLinkPatterns(table, refHeader, altHeader, contextHeader, mutationSymbol,
  reverseComplement, searchPatterns, searchRefHeader, searchAltHeader,
  searchContextHeader, searchIdHeader, searchReverseComplement,
  searchMutationSymbol, checkHeader, searchDistanceHeader,
  linkClustersOnly, renameReverse)

Arguments

table	table with the clusters information
refHeader	Contains the name of the column with the reference nucleotides.
altHeader	Contains the name of the column with the alternative nucleotides.
contextHeader	A string with the name of the column with the context. The data inside this column is e.g. "C.G" hereby stands the "." for the location of the mutation. What symbol is used to describe this location is arbitrary but be sure to adjust the mutationSymbol accordingly when searching for patterns. The contextHeader is irrelevant if linkPatterns is FALSE.
mutationSymbol	A string with the symbol that stands for the mutated nucleotide location in the context. (e.g. "." in "G.C")
reverseComplement	A Boolean to tell if the ref, alt and context needed to be searched with the reverse complement. Irrelevant if searchReverseComplement = TRUE.
searchPatterns	A tibble with the known mutation patterns. The mutationPatterns is the default search table.
searchRefHeader	A string with the column name of the one with the reference nucleotide in the searchPatterns table.
searchAltHeader	A string with the column name of the one with the alternative nucleotide in the searchPatterns table.
searchContextHeader	A string with the column name of the one with the context nucleotide in the searchPatterns table.
searchIdHeader	A string with the column name of the one with the pattern IDs.
searchReverseComplement	A boolean to also search the patterns in the reverse complement of the searchPatterns tibble.
searchMutationSymbol	A string with symbol that stands for the mutated nucleotide location in the column of the searchContextHeader. (e.g. "." in "G.C")
checkHeader	name of the Boolean check column
searchDistanceHeader	A string with the column name of the one with the maximum distance between clustered mutations. Not needed if the distance parameter is NULL. NA's within this column are allowed.
linkClustersOnly	A boolean to tell if only the clustered mutations are needed to be linked with the patterns in the searchPatterns table. When it is FALSE all the mutations will be used.
renameReverse	A Boolean if the id of the process needs to be renamed. This has the effect on the cMut functions that it will no longer treat the reverse complement and non reverse complement as the same. This parameter will irrelevant if searchReverseComplement is FALSE.

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