ilarsf / ukb_data_explorations

ukb_data_explorations

Basic concepts

1. Summarization of UKB fields
2. Summarization of available UKB baskets
3. Data extraction from baskets with instances

Required R libraries

• data.table
• optparse
• parallel
• intervals
• htmltab
• methods
• httr
• readr
• bitops

Step 1: Describe your data

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of your TAB-delimited UKB baskets to a single text file ./data/baskets.txt Add the latest file with withdrawn samples 'w#####_########.csv' to './data/' folder

Step 2: Collectin information about UKB fields

Rscript ./scripts/function.collectFields.r

Step 3: Summarize the available data and prepare data across baskets

Rscript ./scripts/function.summarizeAvailableData.r

Step 4: Extract field information and data and recode with instances:

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