Data representation object

[gregmedlock]

This issue will be for brainstorming implementation details for the object that will store the data type. The general needs/wants for this object are:

• Representing each desired data type in a standardized way
• Function for creating the data object using input data from a project (w/ or w/out peppy)
• Convenience functions for filtering data

Feel free to add design wants/needs and constraints in the comments for this issue.

[dampierch]

Parse Main Goal: take as input some text files, generate as output a loom file
Parse Sub-goal 1: link annotations to measurements (like key-value pairs)
Parse Sub-goal 2: unpack information from sparse matrix into dense matrix

[dampierch]

Note that we have a parse directory where we are storing work related to this task

[dampierch]

We have arbitrarily chosen to start with RNA_mouse_kidney and ATAC_mouse_kidney files (ignoring for now RNA_sciCAR_A549, ATAC_sciCAR_A549, RNA_only_A549, and ATAC_only_A549

[dampierch]

In other words, we are starting with GSM3271044 and GSM3271045 data, saving GSM3271040-GSM3271043 for later