attachMutType {mutSignatures}

Attach Mutation Types.

Description

Modify a data.frame carrying information about DNA mutation, and add a new column that stores formatted multi-nucleotide types.

Usage

attachMutType(
  mutData,
  ref_colName = "reference_allele",
  var_colName = "variant_allele",
  var2_colName = NULL,
  context_colName = "context",
  format = 1,
  mutType_dict = "alexa",
  mutType_colName = "mutType"
)

Arguments

mutData

data.frame including information about DNA mutations

ref_colName

string, pointing to the column with information about the sequence of the "reference_allele"

var_colName

string, pointing to the column with information about the sequence of the "variant_allele"

var2_colName

string (optional), pointing to the column with information about the sequence of a second "variant_allele". Can be NULL

context_colName

string, pointing to the column with information about the nucleotidic "context"

format

integer, indicates the desired mutation type format: (1) N[R>V]N; (2) NN.R>V; (3) R.V[NRN][NVN]

mutType_dict

string, indicates the dictionary to be used for simplifying reverse-complement identical mutation types. It is recommended to use the standard dictionary from COSMIC, by selecting the default value, i.e. "alexa".

mutType_colName

string, column name of the new column added to the data.frame where mutTypes are stored.

Details

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

Value

a data.frame including a new column with mutation Types.

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

 
A <- data.frame(REF = c("A", "T", "G"), 
                VAR = c("G", "C", "C"), 
                CTX = c("TAG", "GTG", "CGA"), 
                stringsAsFactors = FALSE)
mutSignatures::attachMutType(mutData = A, ref_colName = "REF", 
                             var_colName = "VAR", context_colName = "CTX")