createGroupTable: createGroupTable

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

Description

A function to group the table by the cluster IDs and add annotation to it

Usage

createGroupTable(table, clusterIdHeader, refHeader, altHeader,
  contextHeader, mutationSymbol, showWarning)

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.
clusterIdHeader	Contains the name of the column with the cluster IDs.
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")
showWarning	A Boolean if there need to be a warning if nrow is 0.

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