AnVILBrowse: Search AnVIL workspaces using keywords

In shbrief/RunTerraWorkflow: Run workflows implemented in Terra/AnVIL workspace

Search AnVIL workspaces using keywords

Description

Search AnVIL workspaces using keywords

Usage

AnVILBrowse(
  keyword,
  searchFrom = "all",
  returnFrom = NULL,
  metaTables = "default",
  minAge = 0,
  maxAge = 130,
  minCount = 0,
  workspaceTable = NULL,
  workflowTable = NULL,
  dataTable = NULL
)

Arguments

keyword	A character(1). Regular expression is accepted. For example, you can search multiple keywords separated by the vertical bar ("|").
searchFrom	Under the default (all), all the workspaces containing keywords in their workspace/workflow/data will be returned. The other available options are workspace, workflow, and data.
returnFrom	Under the default (NULL), the same data type as for searchFrom will be used, while searchFrom = "all" returns workspaces.
metaTables	Under the default (default), all the publicly accessible AnVIL workspaces will be subjected for search. If you want to search in all the workspaces you have access to, set this argument as custom, and provide the inputs for workspaceTable, workflowTable, and dataTable arguments.
minAge	A numeric (1). Any data with a maximum participant age lower than this parameter will be excluded from the output. Under the default (0), no filtering will be applied. Data entries with no maximum participant age listed will not be removed by this argument.
maxAge	A numeric (1). Any data with a minimum participant age higher than this parameter will be excluded from the output. Under the default (130), no data entries will be removed due to the minimum participant age. Data entries with no minimum participant age listed will not be removed by this argument.
minCount	A numeric (1). Any data with the number of subjects fewer than this parameter will be excluded from the output. Under the default (0), no data entries will be removed due to participant count. Data entries with no participant count listed will not be removed by this argument.
workspaceTable	A data frame. This argument is counted only when metaTables = "custom". Provide the output from the getWorkspaces function, to search in all the workspaces you have access to.
workflowTable	A data frame. This argument is counted only when metaTables = "custom". Provide the output from the getWorkflows function, to search in all the workflows you have access to.
dataTable	A data frame. This argument is counted only when metaTables = "custom". Provide the output from the getData function, to search in all the AnVIL data you have access to.

Value

A data frame of AnVIL resources containing keywords. Depending on the returnFrom argument, it can be workspaces, workflows, or data. Under the default returnFrom = NULL, it returns the same data type as specified in searchFrom or workspace for searchFrom = "all".

Examples

AnVILBrowse("malaria")
AnVILBrowse("resistance")
AnVILBrowse("resistance", searchFrom = "workflow")

shbrief/RunTerraWorkflow documentation built on Oct. 31, 2024, 1:22 p.m.