getAllStudyInfo: Get meta-info of all studies

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method returns meta-info of all studies available in the project directory. In case of cohort studies, both parent and child studies (also called root- and sub-studies) are included.

Usage

getAllStudyInfo(object, ...)

## S4 method for signature 'Commons'
getAllStudyInfo(object, ..., dataStudyOnly = TRUE,
  showAs = "", editor = "")

Arguments

object	Commons class object.
...	There are optional arguments.
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.
showAs	a character string. (optional) When the value is 'table', displays the data as a table through a platform specific table viewer; When it is 'json', displays the json text through a plain text editor; When it is 'text', displays in a brief left-justified text format.
editor	a character string. (optional) The name of your favorite plain text editor. It should be executable from a command-line prompt of the respective platform. For example, notepad (Windows), vim, emacs (Unix), gedit (Ubuntu), nedit (CentOS), etc.

Value

a data frame. The meta-info of all studies. For the table row of a non-cohort study or a parent study in a chort, the root_study and this_study are identical. For the table row of a child- (or sub-) study in a cohort, the this_study column represents the child study, and the root_study column represents the parent study.

Methods (by class)

• Commons: A method of class Commons

Examples

## Not run: 

c <- Commons()
getAllStudyInfo(c)
# or
getAllStudyInfo(c, showAs = 'json', editor = 'notepad')
# or
getAllStudyInfo(c, showAs = 'text', editor = 'gedit')

## End(Not run)

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