dbgaptools

This package assists in creating dataset (DS) and data dictionary (DD) files required for dbGaP submission: sample-subject mapping, sample attributes, and subject consent files. Checks proceed based on dbGaP Submission Guidelines. Additionally, pedigree and phenotype files can be checked for presence of expected subjects.

This package was developed in the context of dbGaP file preparation for the TOPMed Whole Genome Sequencing Program and therefore includes some TOPMed-oriented functionality.

Installation

You can install dbgaptools from github with:

# install.packages("devtools")
devtools::install_github("UW-GAC/dbgaptools")

Types of functions

1. Check functions
   • There are functions to check each dbGaP file type --- DS and, optionally, accompanying DD files
   • See help(check_<ftype>) where ftype includes
     • sattr: for sample attributes
     • ssm: for sample-subject mapping
     • subj: for subject consent
     • pheno: for phenotype
     • ped: for pedigree
   • See also help(check_cross_file) to check consistency across DS files
2. Read functions
   • See help(read_ds_file) and help(read_dd_file)
3. Write functions
   • Convenience functions to write out DS and DD files
   • See help(write_dbgap)