copyUserFile: (internal) Copy decrypted dbGaP files to user project...

In jameslhao/dbgapr_dev: A dbGaP Phenotype Data Organizer

Description

The method copies or moves the decrypted dbgap phenotype files to the project directory. The copied files are organized by study accessions. It is called by the searchCopyPhenoFiles function.

Usage

copyUserFile(object, userFile, ...)

## S4 method for signature 'Commons,character'
copyUserFile(object, userFile = "", ...,
  copyOrMove = "copy", overwrite = F)

Arguments

object	Commons class object
userFile	a character string. The path to decrypted dbGaP phenotype file.
...	There are optional arguments.
copyOrMove	a character string. (optional) If the input string is 'copy' (default), copies the file from a user directory to the project directory. Movis the file if the input string is 'move'.
overwrite	a logical value. (optional) If TRUE, overwrites the file if it already exists in the prject directory; Skip copy if FALSE (default).

Value

(invisible) a character list. The meta-info of copied files.

Methods (by class)

• object = Commons,userFile = character: of class Commons

Examples

## Not run: 

c <- Commons()
file = '/home/foo/data/phs000429.v1.pht002481.v1.p1.c1.areds_data_final_11.EDO.txt.gz' 
copyUserFile(c, userFile = file, overwrite = TRUE) 

## End(Not run)

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