pgSlim-class


This class is a slim version of pgLM and pgFull that does not store any
information pertaining to the actual genes. This means that this class cannot
be the basis for the creation of a pangenome but that pgLM or pgFull objects
can be coerced down to this representation after the pangenome has been 
created to make it less burdensome to work with, while still keeping a lot
of the functionality of the FindMyFriends framework.


A framework for doing microbial comparative genomics in R.
The main purpose of the package is assisting in the creation of
pangenome matrices where genes from related organisms are
grouped by similarity, as well as the analysis of these data.
FindMyFriends provides many novel approaches to doing pangenome
analysis and supports a gene grouping algorithm that scales
linearly, thus making the creation of huge pangenomes feasible.

Thomas Pedersen

FindMyFriends

Microbial Comparative Genomics in R

pgSlim-class function

This class is a slim version of pgLM and pgFull that does not store any
information pertaining to the actual genes. This means that this class cannot
be the basis for the creation of a pangenome but that pgLM or pgFull objects
can be coerced down to this representation after the pangenome has been 
created to make it less burdensome to work with, while still keeping a lot
of the functionality of the FindMyFriends framework.

pgSlim-class: Class for pangenome data with no reference to genes

Description

Arguments

See Also