removeMismatchMut: Remove Mismatched Mutations.

In dami82/mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Remove Mismatched Mutations.

Description

Remove mutation types that do not match the expected nucleotidic context.

Usage

removeMismatchMut(
  mutData,
  refMut_colName = "mutation",
  context_colName = "context",
  refMut_format = "N>N"
)

Arguments

mutData	data.frame including mutation data, as well as the nucleotide context around the mutated position
refMut_colName	string, name of the column storing REF and VAR data. Defaults to "N>N"
context_colName	string, name of the column storing nucleotide context around the variant.
refMut_format	string, format of mutation types. Defaults to "N>N"

Details

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

Value

filtered data.frame

Author(s)

Damiano Fantini, [e-mail]

References

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

1. Official website: http://www.mutsignatures.org

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

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

Examples

x <- mutSignatures:::getTestRunArgs("removeMismatchMut")
y <- mutSignatures:::removeMismatchMut(x,
                                       refMut_colName = "REF",
                                       context_colName = "context",
                                       refMut_format = "N")
y

dami82/mutSignatures documentation built on Jan. 24, 2023, 12:21 a.m.