crawlTcga: Function calls the public or private TCGA http data portals.

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

Description

This function crawls the TCGA public and private data portals. It returns a data frame in which each row is a unique data entity that should be made available in either the public or private SCR.

Usage

crawlTcga(user = "anonymous", pwd = "anonymous", private = FALSE, debug = FALSE)

Arguments

user	Username required to crawl the private portal.
pwd	Password required to crawl the private portal.
private	Logical value. If TRUE then it will crawl the private portal.
writeOut	Logical value. If true the data frame is written out to a file in the current working directory named tcga.txt.
debug	Logical value. If TRUE then it will only crawl the GBM data. Used only for testing.

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 (debug = FALSE, user = "anonymous", pwd = "anonymous", 
    private = FALSE) 
{
    header <- c("study.name\tacronym\ttissue\trepository\tdisease\tspecies\tstudy.numPatients\tdata.url\tdata.name\tdata.md5\tdata.type\tdata.platformName\tdata.status\tdata.add\tdata.lastUpdate\tdata.numSamples\tdata.tcgaLevel")
    if (isTRUE(private)) {
        url <- "https://tcga-data-secure.nci.nih.gov/tcgafiles/tcga4yeo/tumor/"
        write.table(header, file = "tcgaPrivate.txt", quote = FALSE, 
            row.names = FALSE, col.names = FALSE, append = FALSE)
    }
    else {
        url <- "https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/"
        write.table(header, file = "tcga.txt", quote = FALSE, 
            row.names = FALSE, col.names = FALSE, append = FALSE)
    }
    links <- .getLinks(url, debug = debug, user = user, pwd = pwd)
    tcga <- read.table("tcga.txt", sep = "\t", header = TRUE, 
        stringsAsFactors = FALSE)
    return(tcga)
  }

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