getClusterId: getClusterId

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

Description

A function that is able to search for clusters in DNA mutation table (as explained by argument dataTable) in a single chromosome for a single sample.

Usage

getClusterId(dataTable, maxDistance, chromHeader = "Chr",
  sampleIdHeader = "sampleID", positionHeader = "Pos")

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.)

Value

A atomic character vector; contains per index the chromosome nr, sample name and any cluster ID's. For example: Chr1 testSample 1

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