Description Usage Arguments Details Value Author(s) References
View source: R/s03_all_functions.R
Retrieve the nucleotide context around each DNA variant based on the genomic coordinates of the variant and a reference BSGenome database.
1 2 3 4 5 6 7 8 9 | attachContext(
mutData,
BSGenomeDb,
chr_colName = "chr",
start_colName = "start_position",
end_colName = "end_position",
nucl_contextN = 3,
context_colName = "context"
)
|
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" |
This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.
a modified data.frame including the nucleotide context in a new column
Damiano Fantini, damiano.fantini@gmail.com
More information and examples about mutational signature analysis can be found here:
GitHub Repo: https://github.com/dami82/mutSignatures/
More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/
Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/
Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.