search

im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
212 stars 48 forks source link

Can this tool find dN/dS values within regions of a gene? #45

Closed programmingprincess closed 4 years ago

programmingprincess commented 4 years ago

For instance, exon regions, or a particular amino acid sequence that is smaller than a gene--or is gene-level the smallest?

im3sanger commented 4 years ago

Hi Jiaqi Wu,

Thank you for your interest in dNdScv. Yes, this package has functionalities to analyse regions smaller than a gene. There are two main tools that you can use, but please send me an email for more details if you want:

  1. Although it has not been advertised yet, a year ago I added two new functions to the package to study single site and single codon dN/dS: sitednds and codondnds. There is a temporary tutorial on these functions, but we are working to document it better.
  2. The dNdScv package also enables the user to create bespoke RefCDS databases. This means that you can run dNdScv on exons, protein domains, etc. by creating your own reference database. A tutorial on how to do this is here. We already have some of these objects precomputed.

There is also a function to run dNdScv on genesets (genesetdnds). Although most people use dNdScv with default settings, my intention was to create an environment where users can develop more complex applications.

I hope this helps,

Inigo