Read Nexus pathology data

Parse an export from a pathology information system (e.g. Nexus) in either CSV or XML format.

Usage

mp_read_nexus_pathology(path_or_connection)

Arguments

path_or_connection

Character scalar. Path to the CSV or XML export file, or an open connection.

Value

A molpath_parsed object whose data slot is a tibble with columns patient_id, name, dob, sex, sample_id, sample_type, diagnosis, and report_date.

Examples

# \donttest{
nexus_file <- system.file("extdata", "nexus_pathology.csv",
                          package = "molpathR")
if (nzchar(nexus_file)) {
  result <- mp_read_nexus_pathology(nexus_file)
  print(result)
}
# }