checkPhvAccList: (internal) Validate variable accessions

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method validates a given list of the dbGaP variable accessions to make sure each of them is in a right format and belongs to the class study. A new list that have invalid accessions removed is returned.

Usage

checkPhvAccList(object, phvAccList, ...)

## S4 method for signature 'Study,character'
checkPhvAccList(object, phvAccList,
  dataStudyOnly = TRUE)

Arguments

object	Study class object.
phvAccList	a character vector. A list of the dbGaP 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.

Value

a character vector. A validated list of the variable accessions.

Methods (by class)

• object = Study,phvAccList = character: A method of class Study

Examples

## Not run: 

s <- Study(phsAcc = 'phs000001.v3.p1')
accList = c('phv00054119.v1.p1.c2', 'phv00053735.v2', 'phv00053732.v2')
checkPhvAccList(s, phvAccList = accList)

## End(Not run)

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