tests/testthat/test_frequency.R

In progenetix/pgxRpi: R wrapper for Progenetix

context("Retrieve frequency")
require(httr)

test_that("retrieve frequencies with pgxfreq by filter",{
#    url_e1 <- "http://www.progenetix.org/services/intervalFrequencies/?output=pgxseg&filters=43"
    url <- "http://www.progenetix.org/services/intervalFrequencies/?filters=NCIT:C4323,pgx:icdom-85003&output=pgxfreq"
    cat(paste("\n trying:",url,"\n"))
    r <- GET(url)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result  <- read.table(url, header=T, sep="\t"))
    expect_equal(dim(result),c(6212,7))
})


test_that("retrieve frequencies with pgxmatrix by filter",{
    #url_e1 <- "http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C1234"
    url <- "http://www.progenetix.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C4323,pgx:icdom-85003"
    cat(paste("\n trying:",url,"\n"))
    r <- GET(url)
    expect_equal(http_type(r), "text/plain")
    expect_no_error(result  <- read.table(url, header=T, sep="\t"))
    expect_equal(dim(result),c(2,6213))
})

# test_that("retrieve frequencies with pgxmatrix by filter in cellz",{
#     url <- "https://cancercelllines.org/services/intervalFrequencies/?output=pgxmatrix&filters=NCIT:C5228,pgx:icdom-87203"
#     cat(paste("\n trying:",url,"\n"))
#     r <- GET(url)
#     expect_equal(http_type(r), "text/plain")
#     expect_no_error(result  <- read.table(url, header=T, sep="\t"))
#     expect_equal(dim(result),c(2,6213))
# })