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.
bic_file: Required. Synapse ID of the consensus network BIC rda file
output from the consensus network wrapper
temp_storage_loc: Required. The location to store temporary output files.
temp_input_loc: Required. The location to store input files.
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)