filterSNV {mutSignatures}

Filter Single Nucleotide Variants.

Description

Remove entries corresponding to non-SNV, such as insertions and deletions.

Usage

filterSNV(dataSet, seq_colNames)

Arguments

dataSet

data.frame including variant information

seq_colNames

character vector with the names of the columns storing variant data

Details

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

Value

a filtered data.frame only including SNVs

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("filterSNV")
nrow(x)
y <- mutSignatures::filterSNV(dataSet = x, 
                              seq_colNames = c("REF", "ALT"))
nrow(y)