getIdInfo: Get subject, sample, or pedigree information.

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method retrieves either subject, sample, or pedigree information of a given study.

Usage

getIdInfo(object, ...)

## S4 method for signature 'Study'
getIdInfo(object, infoType, ..., colNameWithAcc = FALSE)

Arguments

object	Study class object.
...	There are optional arguments.
infoType	a charcter string. The type of information that is either 'subject', 'sample', or 'pedigree'.
colNameWithAcc	a logical value. (optional) If TRUE, the variable column name is concatenated with the respective variable accession (e.g. AGEPHOT_phv00000027.v2); If FALSE (default), keep the original column name unchanged (e.g. AGEPHOT).

Value

a data frame. The subject, sample, or pedigree info data table.

Methods (by class)

• Study: of class Study

Examples

## Not run: 

s <- Study(phsAcc = 'phs000001.v3.p1')
getIdInfo(s, infoType = 'subject')
# or
s <- Study(phsAcc = 'phs000007.v29')
getIdInfo(s, infoType = 'pedigree')

## End(Not run)

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