crawlNcbiGeo: Crawls the NCBI GEO repository.

In Sage-Bionetworks/rSCR: R functions for contributing to the Synapse Commons Repository

Description

Crawls the NCBI GEO repository to identify available data. Stores the output as an entity in Synapse.

Usage

crawlNcbiGeo()

Value

Returns a synapse entity containing the output of the crawler.

Author(s)

Brig Mecham <[e-mail]>

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function () 
{
    ncbi.input.file <- paste(file.path(.path.package("rSCR"), 
        "extdata"), "/ncbiGPLIDs.txt", sep = "")
    ncbi.perl.crawler <- paste(file.path(.path.package("rSCR"), 
        "Perl"), "/getGSEs.pl", sep = "")
    system(paste("perl", ncbi.perl.crawler, ncbi.input.file))
    geo <- read.table("all.GSEs.txt", sep = "\t", header = TRUE, 
        stringsAsFactors = FALSE, row.names = 1)
    geo <- geo[which(geo$layer.url != "FALSE"), ]
    geo <- .storeGeoInSynapse(geo)
    return(geo)
  }

Sage-Bionetworks/rSCR documentation built on May 9, 2019, 12:13 p.m.