getExtData: (internal) Get the supplemental (external) data

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method returns the supplemental data from the files downloaded from the dbGaP ftp site.

Usage

getExtData(object, type, ...)

## S4 method for signature 'Commons,character'
getExtData(object, type, ..., phsAcc = "",
  dataStudyOnly = TRUE)

Arguments

object	Commons class object.
type	a character string. The object type that is either 'study' (all_study_info), 'dataset' (study_dataset_info), 'variable' (study_variable_info), 'id' (study_id_variable_name), 'code' (study_variable_code_value), or 'manifest' (study_file_manifest).
...	There are optional arguments.
phsAcc	a character string. (optional) The study accession. It is required when the type argument value is not 'study'.
dataStudyOnly	a logical value. When TRUE (default), only downloads the dataset and variable metadata of the stdudies that have data files in the project directory. When FALSE, downloads the dataset and variable metadata of all dbGaP released studies, regardless the actual phenotype data files of the studies are downloaded or not.

Value

a data frame. The meta-data of respective type provided through the input.

Methods (by class)

• object = Commons,type = character: A method of class Commons

Examples

## Not run: 

c <- Commons()
getExtData(c, type = 'study')
# or
getExtData(c, type = 'dataset', phsAcc = 'phs000001.v3')
# or
getExtData(c, type = 'variable', phsAcc = 'phs000001.v3')
# or
getExtData(c, type = 'id', phsAcc = 'phs000001.v3')
# or
getExtData(c, type = 'code', phsAcc = 'phs000001.v3')
# or
getExtData(c, type = 'manifest', phsAcc = 'phs000001.v3')

## End(Not run)

jameslhao/dbgapr_dev documentation built on May 8, 2019, 11:03 p.m.