countMutTypes: Count Mutation Types.

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

Analyze a table (data.frame) including mutation counts. Count and aggregate Count Mutation Types. If multiple samples are included in the same table, results are aggregated by samples.

Usage

countMutTypes(mutTable, mutType_colName = "mutType", sample_colName = NULL)

Arguments

mutTable	data.frame including mutation types and an optional sample ID column
mutType_colName	string, name of the column storing mutTypes
sample_colName	string, name of the column storing sample identifiers. Can be NULL

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

Value

a mutationCounts-class object

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. GitHub Repo: https://github.com/dami82/mutSignatures/

2. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

3. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

4. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

Examples

x <- mutSignatures:::getTestRunArgs("countMutTypes")
x
y <- mutSignatures::countMutTypes(mutTable = x, 
                                  mutType_colName = "mutation", 
                                  sample_colName = "sample")
y

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.