dataDicXmlParser: (internal, deprecated) XML parser of the data dictionary file

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method parses the field values of a given data dictionary XML file. It is called through the function "parseDataDicByStudy".

Usage

dataDicXmlParser(object, xmlFileName, xmlFilePath, phsAcc, ...)

## S4 method for signature 'Commons,character'
dataDicXmlParser(object, xmlFileName, xmlFilePath,
  phsAcc, ..., fileInfoDF = data.frame(), computeType = FALSE)

Arguments

object	Commons class object.
xmlFileName	a character string. The name of the data dictionary XML file.
xmlFilePath	a character string. The path to the directory where the data dictionary XML file is located.
phsAcc	a character string. The dbGaP study accession.
...	There are optional arguments.
fileInfoDF	a data frame. (optional) The copied file info read from the pht_file_info_indiv.json under the ncbi/dbgapr_conf directory. This is needed when computeType is TRUE.
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 set TRUE if it is a large study that have a large number of datasets.

Value

a character string. The path to the resulting rds file of the parsed data dictionary.

Methods (by class)

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

Examples

## Not run: 

c <- Commons()
filename = 'phs000001.v3.pht000001.v2.genspecphenotype.data_dict.xml'
filepath = '/home/foo/my_project/gapwork/data/phs000001/phs000001.v3/data_dict'
dataDicXmlParser(c, xmlFileName=filename, xmlFilePath=filepath, phsAcc='phs000001.v3.p1')

## End(Not run)

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