Data representation object

databio / bdshack19

Coordinating the 2019 Biomedical Data Science Hackathon at UVA

3 stars 3 forks source link

Data representation object #2

Open gregmedlock opened 5 years ago

gregmedlock commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

dampierch commented 5 years ago

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 commented 5 years ago

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