removeMismatchMut {mutSignatures}

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