callSearchclusterPatterns: callSearchclusterPatterns

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

Description

A function to add and change columns of the groupClusters function with the results of the searchClusterPatterns function.

Usage

callSearchclusterPatterns(table, patternIntersect, searchPatterns,
  searchRefHeader, searchAltHeader, searchIdHeader, searchDistanceHeader,
  searchReverseComplement, renameReverse)

Arguments

table	A table with columns containing cluster IDs, reference and alternative nucleotide. See the output of the identifyClusters function for more information about the table.
patternIntersect	A Boolean if the table contains patterns and these needed to be processed as well.
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.
searchIdHeader	A string with the column name of the one with the pattern IDs.
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.
searchReverseComplement	A boolean to also search the patterns in the reverse complement of the searchPatterns tibble.
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.