pgLM-class


This class handles pangenome information where gene sequences are kept on 
disc instead of stored in memory. As long as the original fasta files are
not modified, this class will take care of indexing the genes correctly. This
class has a substantially lower memory footprint than the 
<code>pgFull</code> class at the expense of longer sequence lookup
times. For massive pangenomes containing Gb of sequence data there is no 
alternative though.


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

pgLM-class function

 <dl>
<dt><code>seqIndex</code></dt><dd>A data.frame as produced by 
<code><a rd-options="Biostrings" href="/link/fasta.index?package=FindMyFriends&version=1.2.2&to=Biostrings" data-mini-rdoc="Biostrings::fasta.index">fasta.index</a></code> with random access information for each
gene.</dd> </dl>

Slots

This class handles pangenome information where gene sequences are kept on 
disc instead of stored in memory. As long as the original fasta files are
not modified, this class will take care of indexing the genes correctly. This
class has a substantially lower memory footprint than the 
<code><linkS4class>pgFull</linkS4class></code> class at the expense of longer sequence lookup
times. For massive pangenomes containing Gb of sequence data there is no 
alternative though.

pgLM-class: Class for reference based pangenome data

Description

Arguments

Slots

See Also