check_dd: Check data dictionary (generic)
In UW-GAC/dbgaptools: Creates and Checks Standard Files for dbGaP submission

Description Usage Arguments Details Value

Check data dictionary (generic)

1	.check_dd(dd, ds = NULL, dstype = "")

`dd`	Data dictionary (DD) object
`ds`	Corresponding dataset (DS) object
`dstype`	Type of corresponding DS file, one of "pheno","ped","sattr","ssm","subj."

Data dictionary files can be Excel (.xls, .xlsx) or tab-delimited .txt. The first two columns must be 'VARNAME' and 'VARDESC' in order for checks to proceed. Reports errors or issues with DD file. When the corresponding DS file is also provided, checks for consistency between the two.

Even if DS file is not provided, (ds == NULL), the (dstype) must be specified to check for customize check for UNITS and VALUES columns: pheno = phenotype DS; ped = pedigree DS, sattr =sample attributes DS, ssm=sample-subject mapping DS, subj=subject consent DS. Note VALUES are considered required for pheno, ped, sattr, and subj DS types. Additionally, UNITS are considered required for pheno and sattr DS types. Note some studies may not actually require VALUES and UNITS in these files types, but when missing they are reported out here for convenience.

dd_report, a list of the following issues (when present):

`lowercase`	Logical flag indicating non-uppercase variable names
`missing_reqvars`	Missing and required variables, based on dstype
`extra_vars`	Extra variables
`uniquekey_flags`	Returns warning when UNIQUEKEY column is populated for file types other than phenotype (most common need for UNIQUEKEY) or sample attributes (which in some cases requires UNIQUEKEY). Returns warning if, in pheno or sattr dstypes, the UNIQUEKEY variable(s) do not specify unique rows in the DS.
`vals_warnings`	Vector of warnings about VALUES columns
`missing_dsvars`	Variables present in DS but not defined in DD
`min_errors`	Variables for which DS value are < DD MIN
`max_errors`	Variables for which DS value are > DD MAX
`illegal_vars`	Variable names containing illegal characters: '\', '/', ',' (comma), or 'dbGaP' are present