For the current development, we use a single (default) config profile per file It is divided into four sections :
- Input Profile
- Provenanace
- Output Profile
- Computing Specs
Each of these sections are further divided into subsections and tags that has to be added and required for most cases, else filled as NULL
input_synid
Required. The Synapse ID of the input file is to provided; User has to make sure that their synapse profile has access to this particular profile
project_id
Required. The Synapse ID of the Project folder currently the user owns to build provenance and upload files
na_fill
Required. Value to be filled in case of missing values, else will be omitted from original dataset.
network_method
Required. The type of network methods to be used in a list format with quotes.
- The options in light network include c3net, mrnet, wgcna
- The options in light network include lassoAIC, lassoBIC, lassoCV1se, lassoCVmin, ridgeAIC, ridgeBIC, ridgeCV1se, ridgeCVmin, sparrowZ, sparrow2Z
- The options in light network include genie3 and tigress
p_val_c3net
Optional. P - value threshold for the C3Net method, if specified in network_method, else leave blank or NULL
p_val_mrnet
Optional. P - value threshold for the mrnet method, if specified in network_method, else leave blank or NULL
p_val_wgcna
Optional. P - value threshold for the WGCNA method, if specified in network_method, else leave blank or NULL
temp_storage_loc: Required.Temporary file storage location for the input file which will be deleted after completion of the process
rsquaredCut
Optional. R squared cutt-off for the WGCNA network method and if not used, leave blank or NULL
defaultnaPower
Optional. Default NA power value for WGCNA network method and if not used, leave blank or NULL
Annotations
Provenance annoation subsections - can be obtained from the parent syn ID
More details about obtaining annotations from synapse can be found here
More details on the functioning of Provenance can be found here
A sample annotation profile includes the following required information and can be replaced with NULL if unknown
data_type: ['clinical','geneExpression']
resource_type: metadata
metadata_type: 'analytical covariates'
ismodelsystem: FALSE
ismultispecimen: TRUE
fileformat: csv
grant: U01AG046152
species: Human
organ: brain
tissue: ['dorsolateral prefrontal cortex', 'Head of caudate nucleus', 'posterior cingulate cortex']
study: ["ROSMAP","rnaSeqReprocessing"]
consortium: AMP-AD
assay: rnaSeq
code_annotations For development purpose only. DO NOT CHANGE the code annotations unless user determines to use another analysis pipeline
- repository: PradoVarathan/Reprocessing_Metanetwork_Analysis # The current repository from where the analysis code is obtained from
- ref: branch
- ref_name: main
- repository_path: Network_Wrapper.R # The code block path in the repository used for analysis
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_path
Required. The full path for the final output file
output_name
Required. The output name as to be updated in Synapse Project
md5_output_path
Required. The output path for the md5 formatted output file
error_path
Required. The full path for the error file from the process
light_ncores
Total number of cores available for the light network processing (c3net, mrnet and wgcna) and if not being used, leave blank or NULL
medium_ncores
Total number of cores available for the medium network processing (lassoAIC, lassoBIC, lassoCV1se, lassoCVmin, ridgeAIC, ridgeBIC, ridgeCV1se, ridgeCVmin, sparrowZand sparrow2Z) and if not being used, leave blank or NULL
heavy_ncores
Total number of cores available for the heavy network processing (genie3 and tigress) and if not being used, leave blank or NULL