addOrgInfo: Safely add organisms info

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

This method allows for adding of organism metadata by specifying the name of the metadata and the organisms it should be added to. It protects the user from overwriting information that is derived from the data and ensures proper formatting. Should be prefered to orgInfo<- for all but the simplest cases.

Usage

addOrgInfo(object, ...)

## S4 method for signature 'pgVirtual'
addOrgInfo(object, info, key)

Arguments

object	A pgVirtual subclass
...	parameters passed on.
info	A data.frame with information to add
key	Either an integer vector with the index of each organism the rows in info corresponds to, or the name of the column in info that holds the indexes.

Value

An object of the same class as object with the added organism information.

Methods (by class)

• pgVirtual: Add organism info safely for all pgVirtual subclasses

See Also

Other Metadata: addGroupInfo, groupInfo, orgInfo

Examples

testPG <- .loadPgExample()

# Create some information
info <- data.frame(location=c('Copenhagen', 'Paris', 'London'), 
    name=c('AE017243', 'AP012303', 'AE017244')
)

# Add the information
testPG <- addOrgInfo(testPG, info=info, key='name')

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