In Sage-Bionetworks/metanetwork: Network meta analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

A configuration file defines the inputs for the Consensus Network Wrapper workflow. Update the default parameters to include the Synapse ID where your data is stored and the appropriate annotation data you want to use for storage of the produced consensus network. The full list of configurable options are:

default:
  input_profile:
    input_folderid:         Required. A character vector of a synapse ID of a 
                            synapse project/folder that consists of all the 
                            individual network folders names with a pattern or
                            just the method name.
    project_id:             Required. The synapse output folder where the 
                            consensus network is stored.
    input_proj_id:          Required. The original input data matrix used to prepare
                            the individual networks themselves, such as 
                            RNAseq data or microarray data.
    is_csv:                 Optional. A logical TRUE/FALSE value specifying if the 
                            original input data matrix used to prepare the individual 
                            networks is a csv (TRUE), or tab delimited file with 
                            the rownames as the first column (FALSE).
                            (Default is TRUE)
    temp_storage_loc:       Required. The location to store temporary output files.
    temp_input_loc:         Required. The location to store input files.
    pattern_id:             Required. A character vector too match the file names 
                            associated to the children entities in project_id.
                            eg( _Network)
    run_id:                 Required. A character vector too match in the children 
                            entities in project_id. This may or may not be the same 
                            as `pattern_id` depending on your network construction 
                            parameters. (eg. Network') 
  provenance:               **Annotations** rovenance annoation subsections - 
                            can be obtained from the parent syn ID. More details 
                            about obtaining annotations from synapse can be found 
                            [here](https://help.synapse.org/docs/Annotations-and-Queries.2011070649.html).
                            More details on the functioning of Provenance can be 
                            found [here](https://help.synapse.org/docs/Provenance.1972470373.html) 
                            A sample annotation profile includes the following required 
                            information and can be replaced with NULL if unknown.

    annotations:
      data_type:            Optional. Type of data. (eg. ['clinical','geneExpression'])
      resource_type:        Optional. Type of resource to surface in data portals (eg. metadata)
      metadata_type:        Optional. Sub-Type of metadata class (eg. 'analytical covariates')
      ismodelsystem:        Optional. Is this data from a model system (eg. FALSE)
      ismultispecimen:      Optional. Is there multiple observations for any 
                            induvidual. (eg. TRUE)
      fileformat:           Optional. File format of the data. (eg. csv)
      grant:                Optional. Is this data generated towards the aim of 
                            a specific grant. (eg. U01AG046152)
      species:              Optional. What species is this data profiled from.
                            (eg. Human)
      organ:                Optional. What organ is this data profiled from.
                            (eg. brain)
      tissue:               Optional. What tissues does this data originate from.
                            (eg. ['A1C','CgG','M1','MTG','S1','V1C'])
      study:                Optional. Is this data associated with a specific study.
                            (eg. ["Allen","SMART-Seq2"])
      consortium:           Optional. Was this data generated for a specific
                            consortia. (eg. AMP-AD)
      assay:                Optional. What is the base data-type. (eg. rnaSeq)
    code_annotations:       For development purpose only. **DO NOT CHANGE** the code 
                            annotations unless user determines to use another analysis pipeline
        repository:         Required The current repository from where the analysis 
                            code is obtained from. (eg. Sage-Bionetworks/metanetwork)
        ref:                Required The type of pointer to use for the repo commit 
                            history. (eg. branch)
        ref_name:           Required The name of pointer type to use for the repo 
                            commit history ie the name of the branch. (eg. main or master)
        repository_path:    Required The current repository from where the analysis 
                            code is obtained from. eg(. inst/runscripts/Consensus_Wrapper.R)
    activity_name:          Required. The activity name for Synapse Provenance path creation 
    activity_description:   Required. Detailed explanation of the activity in quotes 
                            to be updated on Synapse  
  output_profile:
    output_path:            Required. The full path for the final output file. (eg. Consensus)
    md5_output_path:        Required. The output MD5 name as to be updated in Synapse 
                            Project (eg. Consensus_md5.out)
    output_name:            Required. The output name as to be updated in Synapse 
                            Project. (eg. 'Consensus Network')
    error_path:             Required. The full path for the error file from the 
                            process (eg. /root/error)

Sage-Bionetworks/metanetwork documentation built on April 27, 2022, 7:42 a.m.