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

Description Usage Arguments Value Examples

View source: R/downloadPc2.R

Description

Download Pathway Commons files (uses menu and cache)

Usage

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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 file.path(Sys.getenv("HOME"), ".paxtoolsRCache")

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

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## 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)
  

cannin/paxtoolsr documentation built on Sept. 12, 2019, 1:43 p.m.