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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.