Difference between revisions of "UK Biobank/Downloading the data"
Jump to navigation
Jump to search
(Created page with "# The phenotype file was downloaded from UK Biobank by the project PI as instructed in the data accessibility email. # All of the utilities from the UK Biobank [http://biobank...") |
|||
| Line 1: | Line 1: | ||
| − | + | These procedures were all derived from the [http://biobank.ctsu.ox.ac.uk/showcase/exinfo.cgi?src=accessing_data_guide documentation] at the UK Biobank. | |
| − | + | ||
| − | + | == Phenotypic data == | |
| − | + | ||
| − | < | + | <ol> |
| + | <li>The phenotype file was downloaded from UK Biobank by the project PI as instructed in the data accessibility email.</li> | ||
| + | <li>All of the utilities from the UK Biobank [http://biobank.ctsu.ox.ac.uk/showcase/download.cgi download] page were retrieved.</li> | ||
| + | <li>The key, k1234.key was saved from the PI's email.</li> | ||
| + | <li> This command was run to decrypt the downloaded phenotype file | ||
| + | <pre> | ||
$ ./ukb_unpack ukb1234.enc k1234.key | $ ./ukb_unpack ukb1234.enc k1234.key | ||
| − | </ | + | </pre> |
| − | which produced the file ukb1234.enc_ukb | + | which produced the file ukb1234.enc_ukb</li> |
| + | <li>Once decrypted, the following commands were run to extract the data into useful formats | ||
| + | <pre> | ||
| + | $ ./ukb_conv ukb1234.enc_ukb bulk -eencoding.ukb | ||
| + | $ ./ukb_conv ukb1234.enc_ukb docs -eencoding.ukb | ||
| + | $ ./ukb_conv ukb1234.enc_ukb r -eencoding.ukb | ||
| + | </pre> | ||
| + | <ol> | ||
| + | <li>bulk is a list of IDs for use with the ukbfetch utility</li> | ||
| + | <li>docs produces an html file containing [https://ibg.colorado.edu/~lessem/ukb6395.html documentation of the variables] in this dataset</li> | ||
| + | <li>r produces a tab deliminated file and an R script for labeling and putting levels on the variables. | ||
| + | </ol> | ||
| + | </li> | ||
| + | </ol> | ||
| + | |||
| + | |||
| + | == Genotypic data == | ||
| + | <ol> | ||
| + | |||
| + | </ol> | ||
Revision as of 22:49, 19 February 2016
These procedures were all derived from the documentation at the UK Biobank.
Phenotypic data
- The phenotype file was downloaded from UK Biobank by the project PI as instructed in the data accessibility email.
- All of the utilities from the UK Biobank download page were retrieved.
- The key, k1234.key was saved from the PI's email.
- This command was run to decrypt the downloaded phenotype file
$ ./ukb_unpack ukb1234.enc k1234.key
which produced the file ukb1234.enc_ukb - Once decrypted, the following commands were run to extract the data into useful formats
$ ./ukb_conv ukb1234.enc_ukb bulk -eencoding.ukb $ ./ukb_conv ukb1234.enc_ukb docs -eencoding.ukb $ ./ukb_conv ukb1234.enc_ukb r -eencoding.ukb
- bulk is a list of IDs for use with the ukbfetch utility
- docs produces an html file containing documentation of the variables in this dataset
- r produces a tab deliminated file and an R script for labeling and putting levels on the variables.