snvTabToDNVcatalogue: Build a Dinucleotide Variants Catalogue from SNVs
In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib
View source: R/DinucleotideVariantsLib.R
snvTabToDNVcatalogue R Documentation
Build a Dinucleotide Variants Catalogue from SNVs
Description
This function takes as input a list of single nucleotide variants (SNVs),
and computes a list of dinucleotide variants (DNVs) finding which SNVs
are next to each other. It then returns the annotated DNVs and the DNV catalogues.
The catalogues are in Zou's style.
Usage
snvTabToDNVcatalogue(snvtab)
Arguments
snvtab
requires columns Sample, Chrom, Pos, Ref, Alt, with Ref and Alt of length 1
Value
list of DNVs and DNV catalogue
References
J. E. Kucab, X. Zou, S. Morganella, M. Joel, A. S. Nanda, E. Nagy, C. Gomez, A. Degasperi, R. Harris, S. P. Jackson, V. M. Arlt, D. H. Phillips, S. Nik-Zainal. A Compendium of Mutational Signatures of Environmental Agents. Cell, https://doi.org/10.1016/j.cell.2019.03.001, 2019.
Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
View source: R/DinucleotideVariantsLib.R
| snvTabToDNVcatalogue | R Documentation |
Build a Dinucleotide Variants Catalogue from SNVs
Description
This function takes as input a list of single nucleotide variants (SNVs), and computes a list of dinucleotide variants (DNVs) finding which SNVs are next to each other. It then returns the annotated DNVs and the DNV catalogues. The catalogues are in Zou's style.
Usage
snvTabToDNVcatalogue(snvtab)
Arguments
snvtab |
requires columns Sample, Chrom, Pos, Ref, Alt, with Ref and Alt of length 1 |
Value
list of DNVs and DNV catalogue
References
J. E. Kucab, X. Zou, S. Morganella, M. Joel, A. S. Nanda, E. Nagy, C. Gomez, A. Degasperi, R. Harris, S. P. Jackson, V. M. Arlt, D. H. Phillips, S. Nik-Zainal. A Compendium of Mutational Signatures of Environmental Agents. Cell, https://doi.org/10.1016/j.cell.2019.03.001, 2019.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.