check_subj: Check subject consent file
In UW-GAC/dbgaptools: Creates and Checks Standard Files for dbGaP submission

Description Usage Arguments Details Value

View source: R/check_functions.R

Check contents of a subject consent file for dbGaP posting.

1
2
3

check_subj(dsfile, ddfile = NULL, na_vals = c("NA", "N/A", "na",
  "n/a"), subj_exp = NULL, subjectID_col = "SUBJECT_ID",
  consent_col = "CONSENT")

`dsfile`	Path to the data file on disk
`ddfile`	Path to the data dictionary file on disk
`na_vals`	Vector of strings that should be read in as NA/missing in data file (see details of `read_ds_file`)
`subj_exp`	Dataframe of expected subject ID (column 1) and consent value (column 2)
`subjectID_col`	Column name for subject-level ID
`consent_col`	Column name for consent variable

The subject consent file should be a tab-delimited .txt file. When (subj_exp != NULL), checks for presence of expected subject IDs, and correspondence between subject ID and consent value. If only one of either SUBJECT_SOURCE and SOURCE_SUBJECT_ID is present, returns a warning indicating that both variables must be submitted together. Checks that all consent groups are coded using an integer (1, 2, 3, etc).

If a data dictionary is provided (ddfile != NULL), additionally checks for agreement between data file and data dictionary. Assumes that CONSENT=0 need not be defined in data dictionary, as dbGaP automatically codes as subjects used as genotyping controls and/or pedigree linking members. Data dictionary files can be Excel (.xls, .xlsx) or tab-delimited .txt.

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

`consent_varname`	Logical, indicating consent variable is not named 'CONSENT'
`alias_missvar`	Logical, indicating when only one of SUBJECT_SOURCE or SOURCE_SUBJECT_ID is submitted
`dd_errors`	Differences in fields between data file and data dictionary
`dup_subjects`	List of duplicated subject IDs
`extra_subjects`	Subjects in data file missing from `subj_exp`
`missing_subjects`	Subjects in `subj_exp` missing from data file
`consent_diffs`	Discrepancies in correspondence between subject ID and consent. Lists entries in `subj_exp` that disagree with correspondence in the data file
`consent_nonints`	List of non-integer consent values.
`potential_pheno_vars`	List of potential phenotype variable names in DS. Note phenotype should only be in one of these two files: phenotype file or subject consent file.