getVariableInfoByPhvAcc: (internal) Get variable meta-info by accession

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method returns the variable meta-info as a data frame given the variable accession.

Usage

getVariableInfoByPhvAcc(object, phvAccList, ...)

## S4 method for signature 'Study,character'
getVariableInfoByPhvAcc(object, phvAccList, ...,
  dataStudyOnly = TRUE, showTable = F, showBrief = T, validateInput = T)

Arguments

object	Study class object.
phvAccList	a character vector. The dbGaP phenotype variable accessions.
...	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.
showTable	(optional) a logical value. If TRUE, displays the variable meta-info in a platform specific table viewer; Not display if FALSE (default).
showBrief	(optional) a logical value. If TRUE (default), console displays a brief version of the variable info. Not display if FALSE.
validateInput	(optional). If TRUE, checks the input variable accessions to make sure they belong to downloaded data under the user project. No check if FALSE.

Value

a data frame. (invisible) The meta-info of the input variables.

Methods (by class)

• object = Study,phvAccList = character: of class Commons

Examples

## Not run: 

s <- Study(phsAcc = 'phs000001.v3.p1')
accList = c('phv00054119.v1.p1', 'phv00054118.v1.p1', 'phv00000035.v2')
getVariableInfoByPhvAcc(s, phvAccList = accList) 
getVariableInfoByPhvAcc(s, phvAccList = accList, showBrief=T)

## End(Not run)

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