countMutTypes {mutSignatures} | R Documentation |
Count Mutation Types.
Description
Analyze a table (data.frame) including mutation counts. Count and aggregate Count Mutation Types. If multiple samples are included in the same table, results are aggregated by samples.
Usage
countMutTypes(mutTable, mutType_colName = "mutType", sample_colName = NULL)
Arguments
mutTable |
data.frame including mutation types and an optional sample ID column |
mutType_colName |
string, name of the column storing mutTypes |
sample_colName |
string, name of the column storing sample identifiers. Can be NULL |
Details
This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.
Value
a mutationCounts-class object
Author(s)
Damiano Fantini, damiano.fantini@gmail.com
References
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
Examples
x <- mutSignatures:::getTestRunArgs("countMutTypes")
x
y <- mutSignatures::countMutTypes(mutTable = x,
mutType_colName = "mutation",
sample_colName = "sample")
y