Review Notes from Mason:

• I fixed a few minor errors such as spelling errors and I capitalized some proper nouns.

• The information found directly under the section titled "Start IGB" may be more effective if it is less of a paragraph form and in more of a list form.

• R functions such as waitForFile(), IGBfunctions.R, etc. should use bold formatting since this is exact text that can be seen in R.

• I would change this: "Which genes in the test set have more than 3 transcripts?" to something similar to "Use the code below to see genes in the test set that have more than 3 transcripts." (Changed a question into an instruction)

• Some of the instructions above the code blocks seem to be telling the user to do something. I am wondering if these instructions are telling the user that they have to do something to accomplish the overall task or if these instructions are telling the user that they can follow these instructions if they have a need for it. Basically, I am wondering if the blocks of code are supposed to be performed in a specific order or if these are just code snippets that can be used at any time in a user's workflow to perform a small task. Maybe you can find a way to make this clearer, or maybe I am not understanding something.

I am reassigning this story to Ivory to make changes based on my review if she is able to or agrees with my comments.

Bitbucket link https://bitbucket.org/lorainelab/rtoigb

I will follow up with proof reading the content of the markdown and wiki page

IGB User's Guide -> Home -> Advanced Features -> Scripting with R (Draft)
https://wiki.transvar.org/pages/viewpage.action?pageId=37945451

Please proof-read for sense and make sure this generally conforms to the rules about writing for the users guide.
Then pass it to Ann or David to see if this is what they wanted.

This needs to be reviewed before it is made public.