attachContext {mutSignatures}

Attach Nucleotide Context.

Description

Retrieve the nucleotide context around each DNA variant based on the genomic coordinates of the variant and a reference BSGenome database.

Usage

attachContext(
  mutData,
  BSGenomeDb,
  chr_colName = "chr",
  start_colName = "start_position",
  end_colName = "end_position",
  nucl_contextN = 3,
  context_colName = "context"
)

Arguments

mutData

data.frame storing mutation data

BSGenomeDb

a BSGenomeDb-class object, storing info about the genome of interest

chr_colName

string, name of the column storing seqNames. Defaults to "chr"

start_colName

string, name of the column storing start positions. Defaults to "start_position"

end_colName

string, name of the column storing end positions. Defaults to "end_position"

nucl_contextN

integer, the span of nucleotides to be retrieved around the variant. Defaults to 3

context_colName

string, name of the column that will be storing the nucleotide context. Defaults to "context"

Details

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

Value

a modified data.frame including the nucleotide context in a new column

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