orgStat: Calculate statistics about each organism

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method, much like codegroupStat 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.

Usage

orgStat(object, ...)

## S4 method for signature 'pgVirtual'
orgStat(object, subset, getFrequency = FALSE)

Arguments

object	A pgVirtual subclass
...	parameters passed on.
subset	Name or indexes of organisms to include
getFrequency	logical. Should amino/nucleic acid frequency be calculated

Value

A data.frame with a row per organism, with each statistic in a column

Methods (by class)

• pgVirtual: Organism statistics for all pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

orgStats <- orgStat(testPG)

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.