parseDataDicByStudy: (internal, deprecated) Parse data dictionary XML files of a...

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method parses out the values from the data dictionary XML files of the given study. The parsed values are merges into a single data frame, which is further saved to files of various formats (rds, csv, and json). Before calling the function, the data dictionary files of the study should be made available in the data_dic sub-directory under the project directory. Checkout the searchCopyPhenoFiles function for how to move the files to the directory if not. In most of cases, this function is called through parseDataDic.

Usage

parseDataDicByStudy(object, phsAcc, ...)

## S4 method for signature 'Commons,character'
parseDataDicByStudy(object, phsAcc, ...,
  computeType = TRUE)

Arguments

object	Commons class object.
phsAcc	a character string. The dbGaP study accession.
...	There are optional arguments.
computeType	logical value. (optional) If TRUE, compute data type based on data value and include it in the meta-info file. If FALSE, not compute data type. Note: This step is computationally expensive. Do not use it if it is a large study such as Framingham.

Value

(invisible) a data frame. The merged content of the parsed data dictionary files.

Methods (by class)

• object = Commons,phsAcc = character: A method of class Commons

Examples

## Not run: 

c <- Commons()
parseDataDicByStudy(c, phsAcc = 'phs000001.v3.p1') 
parseDataDicByStudy(c, phsAcc = 'phs000007.v27') 

## End(Not run)

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