groupInfo: Get and set information about gene group

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

Description

These methods lets you access the information stored about each gene group and add to it or modify it. Upfront the following columns are present: 'description', 'group', 'paralogue', 'GO', 'EC', 'nOrg' and 'nGenes'. All except 'group', 'nOrg' and 'nGenes' are filled with NA as default. The latter are prefilled with information derived from the grouping itself and should not be modified manually. 'description' is meant to contain a human readable description of the functionality of the gene group, 'GO' should contain GO terms (stored in a list of character vectors) and EC should contain enzyme numbers (again stored as a list of character vectors). There is no check for the validity of the content so it is up to the user to ensure that the terms added are valid. Additional columns can be added at will.

Usage

groupInfo(object)

groupInfo(object) <- value

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

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

Arguments

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

Value

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

Methods (by class)

• pgInMem: Get gene group metadata for pgInMem subclasses

• pgInMem: Set gene group 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, orgInfo

Examples

testPG <- .loadPgExample(withGroups=TRUE)
head(groupInfo(testPG))

groupInfo(testPG)$description[1] <- 'transposase'

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