searchClusterPatterns: searchClusterPatterns

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

Description

A function to search cluster patterns based on reference, variant and distance of the nucleotides within the cluster.

Usage

searchClusterPatterns(groupedClusters, searchPatterns = mutationPatterns,
  searchRefHeader = "ref", searchAltHeader = "alt",
  searchDistanceHeader = "maxDistance", searchIdHeader = "process",
  reverseComplement = FALSE)

Arguments

groupedClusters	Table gained by using the groupClusters function.
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.
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.
searchIdHeader	A string with the column name of the one with the pattern IDs.
reverseComplement	A Boolean to tell if the ref, alt needs to be searched with the reverse complement. Irrelevant if searchClusterPatterns = FALSE or searchReverseComplement = TRUE.

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