createIdentTable: createIdentTable

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

Description

Creates the table with extra annotation about the present clusters

Usage

createIdentTable(dataTable, maxDistance, chromHeader, sampleIdHeader,
  positionHeader, refHeader, altHeader, contextHeader)

Arguments

dataTable	A data.frame or tibble that contains at least chromosome name, sample ID and position information. The data cannot contain any NA. For an example use testDataSet.
maxDistance	A number with the maximum distance between DNA mutations that are defined as being in a cluster.
chromHeader	A string with the name of the column with the chromosome name. (So the data in the column needs to be notated as e.g. "chr2")
sampleIdHeader	A string with the name of the column with the sample ID.
positionHeader	A string with the name of the column with the position of the mutation. (The data in the column needs to be nummeric.)
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.

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