pgFull-class


This class handles pangenome data without gene location information and with
all sequences stored in memory. This makes sequence lookup much faster but
also increases the memory footprint of the object thus making it a bad choice
for very large pangenome with millions of genes.


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

pgFull-class function

 <dl>
<dt><code>sequences</code></dt><dd>Either an AAStringSet or DNAStringSet containing all 
sequences in the pangenome.</dd> </dl>

Slots

This class handles pangenome data without gene location information and with
all sequences stored in memory. This makes sequence lookup much faster but
also increases the memory footprint of the object thus making it a bad choice
for very large pangenome with millions of genes.

pgFull-class: Class for in memory pangenome data

Description

Arguments

Slots

See Also