README.md

R to ImmPort (R2i)

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Tools for preparing ImmPort Submission

Package Structure

data-raw

data

R

Workflow

1. Setup of Accounts and Infrastructure

2. Install R2i package

devtools::install_github("RGlab/R2i")

3. Load package

library(R2i)

4. Work on MetaData

For each of the following templates, use the corresponding vignette to see examples of how to build, write out, and validate the ImmPort-ready tsv files. These are the required common MetaData templates. The templates should be created in the order they are listed below so that they can be correctly cross-referenced. For example, the "basic_study_design" template needs the protocolID assigned in the "protocol" template, so it must be created after.

  1. protocols
  2. basic_study_design
  3. subjects

Other MetaData templates that may apply to your study (also in order for cross-referencing):

5. Work on AssayData

For each assay that was performed you will need to first create "Reagents" and "treatment" templates. Then you will be able to generate an "experimentSamples" template that references User Defined Ids in your reagent and treatment templates. For some, you will also need a "results" template.

For example, if you did an ELISA assay, you would use the following templates:

Assays with result templates:

Assays without result templates: Genotyping Array Mass Spectrometry * Image Histology

6. Upload Files to ImmPort via Aspera

Upload these templates to ImmPort using the Validate Data tab within the appropriate ImmPort workspace. You will need to login and navigate to the Private data section of the website, then look for Validate Data in the top right.

https://immport.niaid.nih.gov/upload/data/uploadDataMain#!/uploadData



RGLab/R2i documentation built on July 30, 2018, 10:14 p.m.