orgInfo: Get and set information about organisms

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

These methods lets you access the information stored about each organism and add to it or modify it. The only information present up front is the number of genes present in each organism. While possible, this information should not be changed manually but through the removeGene functions.

Usage

orgInfo(object)

orgInfo(object) <- value

## S4 method for signature 'pgInMem'
orgInfo(object)

## S4 replacement method for signature 'pgInMem'
orgInfo(object) <- value

Arguments

object	A pgVirtual subclass
value	A data.frame with a row for each organism

Value

In case of the getter a data.frame with organism information.

Methods (by class)

• pgInMem: Get organism metadata for pgInMem subclasses

• pgInMem: Set organism metadata for pgInMem subclasses

Note

Required for subclasses of pgVirtual in order to extend the class system of FindMyFriends

See Also

Other Metadata: addGroupInfo, addOrgInfo, groupInfo

Examples

testPG <- .loadPgExample()
orgInfo(testPG)

orgInfo(testPG)$Genus <- 'Mycoplasma'

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