- Summarization of UKB fields
- Summarization of available UKB baskets
- Data extraction from baskets with instances
- data.table
- optparse
- parallel
- intervals
- htmltab
- methods
- httr
- readr
- bitops
Add the absolute paths (e.g. /driveA/UKB/ukb####.tab
) of your TAB-delimited UKB baskets to a single text file ./data/baskets.txt
Add the latest file with withdrawn samples 'w#####_########.csv' to './data/' folder
Rscript ./scripts/function.collectFields.r
Rscript ./scripts/function.summarizeAvailableData.r
Rscript ./scripts/function.extractUKBdata.r --help
Usage: ./scripts/function.extractUKBdata.r [options]
Options:
-f FIELDS, --fields=FIELDS
Fields to include, separated by commas [default: ]
-d, --data_coding
Enable data coding [default: FALSE]
-o, --only_info
Display only info [default: FALSE]
-k, --keep_instances
Keep instances in the output [default: FALSE]
-r, --recode
Recode variables [default: TRUE]
-p PREFIX, --prefix=PREFIX
Output file prefix. Leave empty for interactive session [default: ]
-h, --help
Show this help message and exit