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.
You can install dbgaptools from github with:
# install.packages("devtools") devtools::install_github("UW-GAC/dbgaptools")
help(check_<ftype>)where ftype includes
help(check_cross_file)to check consistency across DS files
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