downloadPc2: Download Pathway Commons files (uses menu and cache)

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Download Pathway Commons files (uses menu and cache)

Description

Download Pathway Commons files (uses menu and cache)

Usage

downloadPc2(
  selectedFileName = NULL,
  destDir = NULL,
  returnNames = NULL,
  version,
  verbose = FALSE,
  ...
)

Arguments

selectedFileName	a string, a name of a file to skip the the interactive selection
destDir	a string, the destination directory for the file to be downloaded (Default: NULL). If NULL, then file will be downloaded to cache directory at Sys.getenv("PAXTOOLSR_CACHE")
returnNames	return a vector of names matching the given regular expression
version	a version number for a previous version of Pathway Commons data; versions 3 and above. Parameter set as version="8". Available versions "http://www.pathwaycommons.org/archives/PC2/"
verbose	a flag to display debugging information (Default: FALSE)
...	additional parameters to send to corresponding read* methods

Value

an R object using one of the read* methods provided in this package corresponding to the file downloaded

Examples

## Not run: 
  downloadPc2(version="8") 
  downloadPc2(version="8", returnNames="ext.*sif")
  downloadPc2("PathwayCommons.8.inoh.GSEA.hgnc.gmt.gz", version="8", verbose=TRUE)

## End(Not run)
  

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.