getVariableDataByPhvAccAndSubjId: (internal) Get variable data subset by subject ids

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method returns the data of a given list of variables subset by a list of subject ids.

Usage

getVariableDataByPhvAccAndSubjId(object, phvAccList, ...)

## S4 method for signature 'Study,character'
getVariableDataByPhvAccAndSubjId(object, phvAccList,
  ..., dbgapIdsOrFile = NULL)

Arguments

object	Study class object
phvAccList	a character vector. A list of dbGaP variable accessions.
...	There are optional arguments.
dbgapIdsOrFile	a character vector or a character string. (optional) This argument can be either a vector of ID list or a path to a file that contains a list of IDs. The IDs can be dbGaP_Subject_ID or dbGaP_Sample_ID denpending on type of the data. When the list of IDs is provided by a file, it should be a plain text file with one ID per line.

Value

a data frame. The variable data of given variables subset by the given subjects.

Methods (by class)

• object = Study,phvAccList = character: returns a dataframe of the variable data

Examples

## Not run: 

s <- Study(phsAcc = 'phs000001.v3.p1')
ids <- c("219", "220", "221") 
accList <- c('phv00054119.v1.p1.c2', 'phv00053735.v2')
getVariableDataByPhvAccAndSubjId(s, phvAccList = accList, dbgapIdsOrFile = ids)
idFile = '/home/user/temp/subj_ids.txt'
getVariableDataByPhvAccAndSubjId(s, phvAccList = accList, dbgapIdsOrFile = idFile)

## End(Not run)

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