Overview

This is an R package designed to help the process of phenotype dataset cleaning be automated, rigorous, and transparent. The overall cleaning process is simplified as follows:

• A phenotype spreadsheet is exported to any of several supported formats:

  • .tsv (plaintext, tab-delimited)

  • .dta (STATA format)

  • .sas7bdat (SAS format, with accompanying .sas code for category labels)

  • .zsav (SPSS format)

• The phenotype dataset is configured in YAML format. This allows the user to specify the expected data type (binary, categorical, ordinal, numeric, date, blood pressure, string), boundary conditions for numeric values, levels and alias for binary/categorical/ordinal variables, special values to be encoded as NA (missing) entries, and other restrictions.

• The entire cleaning process for the file is run with a single R command.

• After cleaning is complete, an HTML format report is emitted, reporting summary statistics and data cleaning observations (e.g. invalid values detected for categorical variables); this file is both for recordkeeping and for helping the user improve configuration for more refined cleaning.

Source code is located here.