Function reference • metaboWorkflows

All functions

filePaths() `filePaths<-`() sampleInformation() `sampleInformation<-`(): FilePathInput get and set accessors

FilePathInput-class: S4 class for storing file path input information

instrument() `instrument<-`() directory() `directory<-`() host() `host<-`() port() `port<-`() auth() `auth<-`(): GroverInput get and set methods

GroverInput-class: S4 class for storing grover input information

projectName() `projectName<-`() path() `path<-`() renv() `renv<-`() docker() `docker<-`() github() `github<-`() private() `private<-`() githubActions() `githubActions<-`() parallelPlan() `parallelPlan<-`() force() `force<-`(): Project class get and set methods

Project-class: S4 class to store project directory definitions

name() `name<-`() command() `command<-`() type() `type<-`() args() `args<-`() comment() `comment<-`() code(): Target class get and set methods

Target-class: S4 class to store a target definition

type(<Workflow>) `type<-`(<Workflow>) input() `input<-`() targets() `targets<-`() modules() filePaths(<Workflow>) `filePaths<-`(<Workflow>) sampleInformation(<Workflow>) `sampleInformation<-`(<Workflow>) instrument(<Workflow>) `instrument<-`(<Workflow>) directory(<Workflow>) `directory<-`(<Workflow>) host(<Workflow>) `host<-`(<Workflow>) port(<Workflow>) `port<-`(<Workflow>) auth(<Workflow>) `auth<-`(<Workflow>): Workflow class get and set methods

availableWorkflows(): Available workflows

defineProject(): Define a project directory

defineWorkflow(): Define a metabolomics workflow

generateWorkflow(): Generate a workflow project directory

glimpse(): Visualise the workflow targets

inputFilePath(): Workflow input using file paths

inputGrover(): Workflow input using a grover API

manifest(): Workflow definition target information

target(): Create a workflow target definition

targetsWorkflow() targetsInput() targetsSpectralProcessing() targetsPretreatment() targetsMFassignment() targetsModelling() targetsCorrelations() targetsReport(): Workflow pipeline targets

validate(): Validate a workflow definition

moduleReplace() modulesRemove() modulesKeep() moduleAdd() targetReplace() targetRemove() targetAdd(): Edit workflow targets and modules