data-raw/readme.md

In AllenInstitute/hbadata: Human Brain Atlas Expression Data

The data-raw directory

This directory contains the three scripts used to create the data in this package. The content of this directory should be:

• formatterHBA-0.0.4.r
• concatenate_results.sh
• create_factors.py
• readme.md

Using the Scripts

In order to use these scripts, you'll first need to download the raw data from the Allen Institute. The data comes as 6 large zip file. Uncompress each of them and then place all 6 into a base directory:

cwd
   |_dirHBA
           |_ donor1
           |_ donor2
           |_ ...

All of these scripts can then be run in cwd

formatterHBA-0.0.4.r

This script is the heavy lifter of the three. It creates a new directory in cwd and puts a reformatted version of the data from the donor files into it. The function requires that you go and change the dirHBA variable to run it. This is clearly annotated in the script. After running the script you cwd should look like this

cwd
   |_resultFrameCollapse
   |                    |_ resultFrame1.csv
   |                    |_ resultFrame2.csv
   |                    |_ ...
   |_dirHBA
           |_ donor1
           |_ donor2
           |_ ...

concatenate_results.sh

This script concatentates the resulting csvs from formatterHBA-0.0.4.r together to create one large csv, resultFrameTotal.csv. This script should be run in the current workign directory as follows

$ bash concatenate_results.sh

Currently there is no Windows Equivalent. However, it does run in cygwin.

After running, you cwd should look like

cwd
   |_resultFrameCollapse
   |                    |_ resultFrame1.csv
   |                    |_ resultFrame2.csv
   |                    |_ ...
   |
   |_dirHBA
   |       |_ donor1
   |       |_ donor2
   |       |_ ...
   |
   |_resultFrameTotal.csv

create_factors.py

This script scrapes through each csv in the original donor files and creates a new directory with the unique entries of donors, probes, genes, and structures.

Use this script in the cwd by calling python

$ python create_factors.py

After running, your cwd will look like

cwd
   |_ resultFrameTotal.csv
   |
   |_ resultFrameCollapse
   |                    |_ resultFrame1.csv
   |                    |_ resultFrame2.csv
   |                    |_ ...
   |
   |_ factorsHBA
   |           |_ donors.txt
   |           |_ genes.txt
   |           |_ probes.txt
   |           |_ structure_acronyms.txt
   |           |_ structure_IDs.txt
   |
   |_ dirHBA
           |_ donor1
           |_ donor2
           |_ ...

AllenInstitute/hbadata documentation built on May 6, 2019, 2:18 p.m.