getVarNameAccCombos: (internal) Get concatenated variable name and accession combo...

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method returns a list of concatenated combo strings of variable name and accession given a data dictionary. When dealing with large phvAccList, it is important to set checkList FALSE. Otherwise the process takes will take too long to finish.

Usage

getVarNameAccCombos(object, phvAccList, ...)

## S4 method for signature 'Study,character'
getVarNameAccCombos(object, phvAccList, ...,
  studyDataDicDF = data.frame(), checkList = TRUE)

Arguments

object	Study class object.
phvAccList	a character vector. A list of the dbGaP variable accessions.
...	There are optional arguments.
studyDataDicDF	a data frame. (optional) Study variable meta-info (data dictionary).
checkList	a logical value. (optional) If TRUE, check the input phvAccList. Not check if FALSE.

Value

a character vector. The concatenated combo strings of the variable name and accession.

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')
getVarNameAccCombos(s, phvAccList = accList)

## End(Not run)

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