dbgap.expand: De-aggregate the variable in the datatables and create the...

In hms-dbmi/sandboxR: Create Sandboxes of Phenotypics Data From dbGap

Description

This function extracts informations from .txt.gz files ind dbgap. It will de-agregate the datatables to create one csv file per variable with 2 columns (dbgap_ID and variable_name), and sort them in one folder per datatable. It also creates the first mapping file ("0_map.csv).

Usage

dbgap.expand(phs, files, destination, study_name = phs)

Arguments

phs	dbGap study ID in the for of phsxxxxxx
files	Vector containing the pathways of the folders where the .txt files (or .txt.gz) are located for each consent groups that you want to extract
destination	Pathway to the folder where you want to create the mapping file
study_name	Nickname used for this study. Optional, otherwise will use the phs name

Value

a mapping file (0_map.csv), and a folder (study_tree) with the tree structure of your sandboxes. Also create a hidden file to copy oldmaps (.oldmaps)

Author(s)

Gregoire Versmee, Laura Versmee

hms-dbmi/sandboxR documentation built on May 12, 2019, 1:36 a.m.