getVarNameByPhvAcc: (internal) Get variable names given accessions

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method takes a list of variable accessions and returns a list of variable names. The output variable name can be shown in three different formats: name only ( e.g. LNUCSCORE ), name and accession separated by underscore (e.g. LNUCSCORE_phv00000006.v2), name and accession separated with space and parenthesis (e.g. LNUCSCORE (phv00000006.v2)). There is no validation applied to the input accessions.

Usage

getVarNameByPhvAcc(object, phvAccList, ...)

## S4 method for signature 'Commons,character'
getVarNameByPhvAcc(object, phvAccList, ...,
  colNameWithAcc = F, underscore = F, phsAcc,
  studyDataDicDF = data.frame())

Arguments

object	Commons class object.
phvAccList	a character vector. The dbGaP phenotype variable accessions.
...	There are optional arguments.
colNameWithAcc	a logical value. (optional). If FALSE (default), outputs variable name only; If TRUE, outputs concatenated variable name and variable.
underscore	a logical value. (optional) Used only when colNameWithAcc is TRUE. If TRUE (default), underscore is used between variable name and accession( e.g. LNUCSCORE_phv00000006.v2 ); If FALSE, the parenthesis with a space is used between variable name and accession ( e.g. LNUCSCORE (phv00000006.v2) ).
phsAcc	a character string. (optional) The accession of the study where the variables belong. It is required if studyDataDicDF is not provided.
studyDataDicDF	a data frame. (optional) The data frame of the study data dictionary (variable meta-data). It is required if phsAcc is not provided.

Value

a named list of variable names. The variable names of the input variable accession.

Methods (by class)

• object = Commons,phvAccList = character:

Examples

## Not run: 

c <- Commons()
accList = c('phv00000027.v2', 'phv00053747.v2')
phsAcc = 'phs000001.v3.p1'
getVarNameByPhvAcc(c, phvAccList=accList, phsAcc=phsAcc) 
# or
getVarNameByPhvAcc(c, phvAccList=accList, phsAcc=phsAcc, colNameWithAcc=T)
# or
getVarNameByPhvAcc(c, phvAccList=accList, phsAcc=phsAcc, colNameWithAcc=T, underscore=T)

## End(Not run)

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