orgStat

orgStat,pgVirtual-method

object

subset

logical. Should amino/nucleic acid frequency be 
calculated

getFrequency


This method, much like code<a rd-options="" href="/link/groupStat?package=FindMyFriends&version=1.2.2" data-mini-rdoc="FindMyFriends::groupStat">groupStat</a> calculates different 
statistics for each organism in the pangenome. Depending on the parameters
the statistics are: number of genes, minimum length of gene, maximum length
of gene standard deviation of gene lengths, residue frequency, number of gene
groups and number of paralogues.


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

orgStat function

<ul>
<li> <code>pgVirtual</code>: Organism statistics for all pgVirtual subclasses
</li>
</ul>

Methods (by class)

This method, much like {code{<a href="groupStat" rd-options="">groupStat</a>}} calculates different 
statistics for each organism in the pangenome. Depending on the parameters
the statistics are: number of genes, minimum length of gene, maximum length
of gene standard deviation of gene lengths, residue frequency, number of gene
groups and number of paralogues.

orgStat: Calculate statistics about each organism

Description

Usage

Arguments

Value

Methods (by class)

Examples